additional formatting of F-related material

13output.tex

@@ -91,7 +91,7 @@ \subsubsection{Metrics for Fishing Mortality}
 
 Yr Seas Seas\_dur F\_std annual\_F annual\_M <each fleet's F\_scalar>
 
-In this table, the displayed value for annual\_F will be from the $F=Z-M$ method regardless of which option was chosen for $F\text{\_std}$. If $F\text{\_std}$ uses option 4 or 5, then the annual\_F will use the same range of ages. Otherwise, annual\_F will be for the age that is the mid-age of the age range of the model.
+In this table, the displayed value for $\text{annual\_}F$ will be from the $F=Z-M$ method regardless of which option was chosen for $F\text{\_std}$. If $F\text{\_std}$ uses option 4 or 5, then the $\text{annual\_}F$ will use the same range of ages. Otherwise, $\text{annual\_}F$ will be for the age that is the mid-age of the age range of the model.
 
 %The options are:
 %\begin{itemize}
@@ -114,12 +114,20 @@ \subsubsection{Metrics for Fishing Mortality}
 
 \myparagraph{$F\text{-at-Age}$}
 $F\text{-at-Age}$ for each fleet is presented in report.sso as table 39. Its header looks like:
-F\_AT\_AGE report:39
-Area Fleet Sex Morph Yr Seas Era 0 1 2
-
-In addition to the $F\_std$ and annual\_F outputs, info on total $F\text{-at-Age}$ across all fleets is reported at the end of the report.sso file. This section of the report calculates $Z\text{-at-Age}$ as $ln(N_{a+1,t+1}/N_{a,t})$. This is done for numbers at the beginning of each year and the N values are summed over all areas. It is done once using the fishing intensities as estimated (to get $Z\text{-at-Age}$), and once with the $F$ intensities set to 0.0 to get $M\text{-at-Age}$. This latter sequence also provides a measure of dynamic Bzero. The user can then subtract the table of $M\text{-at-Age/year}$ from the table of $Z\text{-at-Age/year}$ to get a table of $F\text{-at-Age/year}$. From this $\text{apical\_}F$, average F over a range of ages, or other user-desired statistics could be calculated. The header for this table looks like:
-Z\_AT\_AGE\_Annual\_2 With\_fishery
-Bio\_Pattern Sex Yr  0 1 2
+\begin{quote}
+	\begin{verbatim}
+	F\_AT\_AGE report:39
+	Area Fleet Sex Morph Yr Seas Era 0 1 2
+	\end{verbatim}
+\end{quote}
+
+In addition to the $F\_std$ and $\text{annual\_}F$ outputs, info on total $F\text{-at-Age}$ across all fleets is reported at the end of the report.sso file. This section of the report calculates $Z\text{-at-Age}$ as $ln(N_{a+1,t+1}/N_{a,t})$. This is done for numbers at the beginning of each year and the N values are summed over all areas. It is done once using the fishing intensities as estimated (to get $Z\text{-at-Age}$), and once with the $F$ intensities set to 0.0 to get $M\text{-at-Age}$. This latter sequence also provides a measure of dynamic Bzero. The user can then subtract the table of $M\text{-at-Age/year}$ from the table of $Z\text{-at-Age/year}$ to get a table of $F\text{-at-Age/year}$. From this $\text{apical\_}F$, average F over a range of ages, or other user-desired statistics could be calculated. The header for this table looks like:
+\begin{quote}
+	\begin{verbatim}
+	Z\_AT\_AGE\_Annual\_2 With\_fishery
+	Bio\_Pattern Sex Yr  0 1 2
+	\end{verbatim}
+\end{quote}
 
 A more detailed report provides $Z$ for each area, bio group (sex, morph, platoon) and age. It is titled something like "Report\_Z\_by\_area\_morph\_platoon\_1 No\_fishery". This table is done with and without the $F$ turned on, so that pair pf reports could be processed to get total $F$ by area, bio, age.
 
@@ -158,7 +166,7 @@ \subsubsection{Metrics for Fishing Mortality}
 \myparagraph{Additional Stock Synthesis inputs related to $F$}
 Below is a list of items to consider in terms of units for $F$ in SS3:
 \begin{itemize}
-	\item If F\_ballpark is specified in the control.ss file, its units are the same as $\text{ann}F$, so is not fleet-specific.
+	\item If $F\text{\_ballpark}$ is specified in the control.ss file, its units are the same as $\text{ann}F$, so is not fleet-specific.
 	\item $F$ as parameter values has units of fleet-specific $F'$.
 	\item In the forecast.ss file there is an option to input a vector of $\text{rel}F$ values. These are dimensionless and will be rescaled to sum to 1.0.
 	\item In the forecast.ss file there is an option to specify an $F$ scalar for the forecast. The units of $F$ scalar are the same as the $F\text{mult}$ values calculated in benchmark. There are a full set of options for forecast $F$ scalar that can be selected in the forecast file.

6starter.tex

@@ -4,7 +4,7 @@ \section{Starter File}
 \subsection{Reading the Manual's format}
 SS3 begins by reading the file starter.ss. The starter file contains need information on the names of the control and data files, run conditions, and output specifications. The term COND appears in the ``Typical Value'' column of this documentation (it does not actually appear in the model files), it indicates that the following section is omitted except under certain conditions, or that the factors included in the following section depend upon certain conditions. In most cases, the description in the definition column is the same as the label output to the ss\_new files.
 
-\subsection{Terminology for Fishing Mortality, F}
+\subsection{Terminology for Fishing Mortality, $F$}
 Here we introduce some terminology related to fishing mortality, $F$. This will provide context for some of the quantities that will be read from the starter file and used throughout the document
 
 $f$ is fleet.
@@ -17,17 +17,17 @@ \subsection{Terminology for Fishing Mortality, F}
 
 $F_{t,f,a}$ is fishing mortality at age for fleet $f$. There is no subscript for area because each fleet is defined to operate in only one area.
 
-$F_{t,f}'$ is a fleet's fishing mortality for the age that has selectivity equal to 1.0. This is also termed F' or full\_F in the SS3 system. If your model is using parameters for $F$, then the parameter values are for the $F'$. Note that some selectivity curves, like double normal, are explicit about having a maximum of 1.0. But other curves like logistic and combinations of length-selectivity and growth, may produce an age-selectivity curve that never reaches 1.0 and time-varying non-parametric selectivity will produce values > 1.0 routinely. In all cases, the resultant $F_{t,f,a}$ comes from $F_{t,f}' * s_{t,f,a}$, so the range of the $F'$ compensates for the scale of the $s$.
+$F_{t,f}'$ is a fleet's fishing mortality for the age that has selectivity equal to 1.0. This is also termed F' or $\text{full\_}F$ in the SS3 system. If your model is using parameters for $F$, then the parameter values are for the $F'$. Note that some selectivity curves, like double normal, are explicit about having a maximum of 1.0. But other curves like logistic and combinations of length-selectivity and growth, may produce an age-selectivity curve that never reaches 1.0 and time-varying non-parametric selectivity will produce values > 1.0 routinely. In all cases, the resultant $F_{t,f,a}$ comes from $F_{t,f}' * s_{t,f,a}$, so the range of the $F'$ compensates for the scale of the $s$.
 
-Apical selectivity is the maximum age-specific selectivity and is not explicit in any internal calculation in SS3, it is just for reporting. If selectivity has a maximum value of 1.0, then apical\_F and full\_F are identical.
+Apical selectivity is the maximum age-specific selectivity and is not explicit in any internal calculation in SS3, it is just for reporting. If selectivity has a maximum value of 1.0, then $\text{apical\_}F$ and $\text{full\_}F$ are identical.
 
 Fully-selected age range is not explicitly used in SS3, especially because SS3 applications routinely have multiple fleets with different selectivity patterns that may have little overlap.
 
 Fbar is the average $F$ over a user specified range of ages, implicitly the fully-selected range for the total $F$ from all the fleets. Some SS3 output options will display Fbar.
 
-Annual\_F is essentially the same as Fbar and is an output quantity.
+$\text{Annual\_}F$ is essentially the same as Fbar and is an output quantity.
 
-F\_std is an output quantity that may be based on Annual\_F or other calculated quantities like exploitation rate. Importantly, the output values of F\_std may be presented as a ratio relative to an equivalent benchmark (reference point) quantity; e.g. $F / F_{MSY}$. Further, the variance of F\_std will be calculated and output.
+F\_std is an output quantity that may be based on $\text{annual\_}F$ or other calculated quantities like exploitation rate. Importantly, the output values of F\_std may be presented as a ratio relative to an equivalent benchmark (reference point) quantity; e.g. $F / F_{MSY}$. Further, the variance of $F\text{\_std}$ will be calculated and output.
 
 $C_{t,f}$ is fleet-specific catch in a time step.