diff --git a/6starter.tex b/6starter.tex index b809344e..99d0513d 100644 --- a/6starter.tex +++ b/6starter.tex @@ -244,15 +244,16 @@ \subsection{Starter File Options (starter.ss)} % & & \\ % & & \Tstrut\\ % & & \Tstrut\Bstrut\\ - - \hline + + \pagebreak + % \hline \multicolumn{2}{l}{COND: Seed Value (i.e., 1234)}& \multirow{1}{1cm}[-0.25cm]{\parbox{12.5cm}{Specify a seed for data generation. This feature is not available in versions prior to v.3.30.15 This is an optional input value allowing for the specification of a random number seed value. If you do not want to specify a seed, skip this input line and end the starter file with the check value (3.30).}} \Tstrut\Bstrut\\ & & \\ & & \Bstrut\\ & & \\ - \pagebreak -% \hline +% \pagebreak + \hline \hypertarget{Convert}{3.30} & Model version check value. & \multirow{1}{1cm}[-0.25cm]{\parbox{12.5cm}{A value of 3.30 indicates that the control and data files are currently in v.3.30 format. A value of 999 indicates that the control and data files are in a previous v.3.24 version. The ss\_trans.exe executable should be used and will convert the v.3.24 files the control.ss\_new and data\_echo.ss\_new files to the new format. All ss\_new files are in the v.3.30 format, so starter.ss\_new has v.3.30 on the last line. The mortality-growth parameter section has a new sequence and v.3.30 cannot read a ss.par file produced by v.3.24 and earlier, so ensure that read par file option at the top of the starter file is set to 0. The \hyperlink{ConvIssues}{Converting Files from Stock Synthesis v.3.24} section has additional information on model features that may impede file conversion.}} \Tstrut\Bstrut\\ & & \\ & & \\ diff --git a/7forecast.tex b/7forecast.tex index 66ddaaa8..f84a84f5 100644 --- a/7forecast.tex +++ b/7forecast.tex @@ -199,7 +199,7 @@ \subsection{Forecast File Options (forecast.ss)} & & \Bstrut\\ & & \Bstrut\\ - %\pagebreak % + \pagebreak %\hline \multicolumn{2}{l}{COND -1: Conditional input for annual control rule buffer} & \multirow{1}{1cm}[-0.25cm]{\parbox{12cm}{Year and control rule buffer value. Can enter a value for each year, or starting sequence of years. The final control rule buffer value will apply to all sequent forecast years.}} \\ \multicolumn{1}{r}{2019 0.8} & & \\ @@ -313,8 +313,9 @@ \subsection{Forecast File Options (forecast.ss)} & 2 = Dead catch (retained + discarded); & \\ & 3 = Retained catch; and & \\ & 99 = Input apical F (the apical F value for the model years can be found in the EXPLOITATION section in the Report file). & \Bstrut\\ - - \hline + + \pagebreak + % \hline \multicolumn{1}{l}{COND: == -1} & \multicolumn{2}{l}{Forecasted catches - enter one line per number of fixed forecast year catch} \Tstrut\\ \multicolumn{1}{r}{2012 1 1 1200 2} & \multicolumn{2}{l}{Year \& Season \& Fleet \& Catch or F value \& Basis} \\ \multicolumn{1}{r}{2013 1 1 1400 3} & \multicolumn{2}{l}{Year \& Season \& Fleet \& Catch or F value \& Basis} \\ diff --git a/8data.tex b/8data.tex index f330773a..8505db49 100644 --- a/8data.tex +++ b/8data.tex @@ -111,7 +111,7 @@ \subsection{Terminology} \subsection{Model Dimensions} \begin{center} - \begin{longtable}{p{4cm} p{12cm}} + \begin{longtable}{p{3cm} p{12cm}} \hline \textbf{Value} & \textbf{Description} \Tstrut\Bstrut\\ \hline @@ -246,7 +246,7 @@ \subsection{Bycatch Fleets} \noindent If a fleet above was set as a bycatch fleet (fleet type = 2), the following line is required: \begin{center} \vspace*{-\baselineskip} - \begin{tabular}{p{2.25cm} p{2.65cm} p{2.25cm} p{2.5cm} p{2.5cm} p{2cm}} + \begin{tabular}{p{2.25cm} p{2.5cm} p{2.25cm} p{2.5cm} p{2.5cm} p{2cm}} \multicolumn{6}{l}{Bycatch fleet input controls:} \\ \hline @@ -347,8 +347,7 @@ \subsection{Catch} The format for a 2 season model with 2 fisheries looks like the table below. Example is sorted by fleet, but the sort order does not matter. In data.ss\_new, the sort order is fleet, year, season. \begin{center} - \vspace*{-\baselineskip} - \begin{tabular}{p{2cm} p{3cm} p{2cm} p{3cm} p{3cm}} + \begin{tabular}{p{3cm} p{3cm} p{2cm} p{3cm} p{3cm}} \multicolumn{5}{l}{Catches by year, season for every fleet:} \\ \hline Year & Season & Fleet & Catch & Catch SE \Tstrut\Bstrut\\ @@ -382,8 +381,7 @@ \subsection{Indices} Indices are data that are compared to aggregate quantities in the model. Typically the index is a measure of selected fish abundance, but this data section also allows for the index to be related to a fishing fleet's F, or to another quantity estimated by the model. The first section of the ``Indices'' setup contains the fleet number, units, error distribution, and whether additional output (SD Report) will be written to the Report file for each fleet that has index data. \begin{center} - \vspace*{-\baselineskip} - \begin{tabular}{p{3cm} p{3cm} p{3cm} p{4cm}} + \begin{tabular}{p{3cm} p{3cm} p{4cm} p{4cm}} \multicolumn{4}{l}{Catch-per-unit-effort (CPUE) and Survey Abundance Observations:} \\ \hline Fleet/ & & Error & \Tstrut\\ @@ -547,7 +545,7 @@ \subsection{Mean Body Weight or Length} This is the overall mean body weight or length across all selected sizes and ages. This may be useful in situations where individual fish are not measured but mean weight is obtained by counting the number of fish in a specified sample (e.g., a 25 kg basket). \begin{center} - \begin{tabular}{p{1.75cm} p{1.75cm} p{1.75cm} p{1.75cm} p{1.75cm} p{2cm} p{2cm}} + \begin{tabular}{p{1.75cm} p{1.75cm} p{1.75cm} p{1.75cm} p{1.75cm} p{2cm} p{1cm}} \multicolumn{7}{l}{Mean Body Weight Data Section:} \\ \hline 1 & \multicolumn{6}{l}{Use mean body size data (0/1)} \Tstrut\Bstrut\\ @@ -630,7 +628,7 @@ \subsection{Population Length Bins} \subsection{Length Composition Data Structure} -\begin{tabular}{p{2cm} p{14cm}} +\begin{tabular}{p{2cm} p{13cm}} \multicolumn{2}{l}{Enter a code to indicate whether or not length composition data will be used:} \Tstrut\Bstrut\\ \hline 1 & Use length composition data (0/1/2) \Tstrut\Bstrut\\ @@ -641,7 +639,7 @@ \subsection{Length Composition Data Structure} If the value for fleet is negative, then the vector of inputs is copied to all partitions (0 = combined, 1 = discard, and 2 = retained) for that fleet and all higher numbered fleets. This as a good practice so that the user controls the values used for all fleets. -\begin{tabular}{p{2cm} p{2cm} p{2cm} p{2cm} p{2cm} p{2cm} p{1cm} p{1cm}} +\begin{tabular}{p{2cm} p{2cm} p{2cm} p{2cm} p{2cm} p{2cm} p{1cm}} \multicolumn{7}{l}{Example table of length composition settings when ``Use length composition data'' = 1 (where here} \\ \multicolumn{7}{l}{the first fleet has multinomial error structure with no associated parameter, and the second fleet} \\ \multicolumn{7}{l}{uses Dirichlet-multinomial structure):} \\ @@ -656,7 +654,7 @@ \subsection{Length Composition Data Structure} \end{tabular} -\begin{tabular}{p{1cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm}} +\begin{tabular}{p{1cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm} p{1.5cm}} \multicolumn{9}{l}{Example table of length composition settings when ``Use length composition data'' = 2 (where here} \\ \multicolumn{9}{l}{the -1 in the fleet column applies the first parameter to all partitions for fleet 1 while fleet 2 has} \\ \multicolumn{9}{l}{separate parameters for discards and retained fish):} \\ @@ -936,7 +934,7 @@ \subsection{Conditional Age-at-Length} Conditional age-at-length data are entered within the age composition data section and can be mixed with marginal age observations for other fleets of other years within a fleet. To treat age data as conditional on length, Lbin\_lo and Lbin\_hi are used to select a subset of the total size range. This is different than setting Lbin\_lo and Lbin\_hi both to -1 to select the entire size range, which treats the data entered on this line within the age composition data section as marginal age composition data. \vspace*{-\baselineskip} -\begin{tabular}{p{0.9cm} p{1cm} p{0.9cm} p{0.9cm} p{1.5cm} p{0.9cm} p{0.9cm} p{0.9cm} p{1cm} p{2.4cm}} +\begin{tabular}{p{1cm} p{1cm} p{1cm} p{1cm} p{1.5cm} p{1cm} p{1cm} p{1cm} p{1cm} p{2.5cm}} \multicolumn{10}{l}{} \\ \multicolumn{10}{l}{An example conditional age-at-length composition observations:} \\ \hline @@ -990,7 +988,7 @@ \subsection{Environmental Data} \begin{center} \vspace*{-\baselineskip} - \begin{tabular}{p{1cm} p{3cm} p{3cm} p{4cm}} + \begin{tabular}{p{1cm} p{3cm} p{3cm} p{3cm}} \multicolumn{4}{l}{Parameter values can be a function of an environmental data series:} \\ \hline 1 & \multicolumn{3}{l}{Number of environmental variables} \Tstrut\Bstrut\\