convert a few more apical to full

13output.tex

@@ -100,7 +100,7 @@ \subsubsection{Metrics for Fishing Mortality}
 %	\item 2 = exploitation(Num)
 %	\item 3 = sum(Frates)
 %\end{itemize}
-%The exploitation rates are calculated as the ratio of the total annual catch (in either biomass or numbers as specified) to the summary biomass or summary numbers on January 1. The sum of the $F$ rates is simply the sum of all the $\text{apical\_}F$s. This makes sense if the F method is in terms of instantaneous $F$ (not Pope's approximation) and if there are not fleets with widely different size/age at peak selectivity, and if there is no seasonality, and especially if there is only one area. 
+%The exploitation rates are calculated as the ratio of the total annual catch (in either biomass or numbers as specified) to the summary biomass or summary numbers on January 1. The sum of the $F$ rates is simply the sum of all the $\text{full\_}F$s. This makes sense if the F method is in terms of instantaneous $F$ (not Pope's approximation) and if there are not fleets with widely different size/age at peak selectivity, and if there is no seasonality, and especially if there is only one area. 
 
 %$F\text{\_std}$ is a single annual value based on $\text{ann}F$ and the relationship to $\text{ann}F$ is specified by F\_report\_basis in the starter.ss file. The benchmark $\text{ann}F$ may be used to rescale the time series of $\text{ann}F$s to become a time series of standardized values representing the intensity of fishing, $F\text{\_std}$. The report basis (the available options for the denominator) is selected in the starter file as:
 
@@ -163,7 +163,7 @@ \subsubsection{Metrics for Fishing Mortality}
 	\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.
 	%(-1 = none; 0 = simple; 1 = F\textsubscript{SPR}; 2 = F\textsubscript{MSY} 3 = F\textsubscript{BTGT} or F\textsubscript{0.1}; 4 = Ave F (uses first-last relative F years); and 5 = input annual F scalar). 
-	If the forecast $F$ scalar is set as $F_\text{SPR}$, then SS3 will use $\text{SPR\_}F\text{mult}$ calculated in benchmark and reported in Forecast-report.sso. If user selects the option to input an annual $F$ scalar, option 5, then the value is input on a following line. Whichever method the user selects for forecast $F$ scalar ($F\text{mult}$), SS3 will start the forecast by creating a fleet-specific vector of $\text{apical\_}F$ values from $F\text{mult}*\text{rel}F_f$.
+	If the forecast $F$ scalar is set as $F_\text{SPR}$, then SS3 will use $\text{SPR\_}F\text{mult}$ calculated in benchmark and reported in Forecast-report.sso. If user selects the option to input an annual $F$ scalar, option 5, then the value is input on a following line. Whichever method the user selects for forecast $F$ scalar ($F\text{mult}$), SS3 will start the forecast by creating a fleet-specific vector of $\text{full\_}F$ values from $F\text{mult}*\text{rel}F_f$.
 	\item Also in the forecast.ss file, the last section of inputs allows for input of time and fleet specific $F_{t,f}'$ values that override the basic forecast $F$ specification described above.
 \end{itemize}
 

6starter.tex

@@ -17,9 +17,9 @@ \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\_scalar 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 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 F\_scalar 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 apical\_F and 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.
 

7forecast.tex

@@ -312,7 +312,7 @@ \subsection{Forecast File Options (forecast.ss)}
     & -1 = Read basis with each observation, allows for a mixture of dead, retained, or F basis by different fleets for the fixed catches below; & \\
     & 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\\
+    & 99 = Input full_F (the full_F value for the model years can be found in the EXPLOITATION section in the Report file). & \Bstrut\\
 
   \pagebreak
   % \hline