update lambdas

9control.tex

@@ -2339,7 +2339,7 @@ \subsubsection{Two-Dimensional Auto-Regressive Selectivity (2DAR; Semi-parametri
 	1 \Tstrut & Two-dimensional auto-regressive selectivity: \\
 	  & 0 = Not used, \\
 	  & 1 = Use 2DAR. \\
-	COND = 1 & Then read a specification line for the first fleet that uses 2DAR, then any short parameter lines invoked by those specifications, then enter another specification for next fleet using 2DAR (if any) and its parameter lines, then finish with a specification line containing negative value for the fleet \Bstrut\\
+	COND = 1 & Then read a specification line for the first fleet that uses 2DAR, then any short parameter lines invoked by those specifications, then enter another specification for next fleet using 2DAR (if any) and its parameter lines, then finish with a specification line containing negative value for the fleet. \Bstrut\\
 	\hline
 \end{tabular}
 
@@ -2383,22 +2383,22 @@ \subsubsection{Two-Dimensional Auto-Regressive Selectivity (2DAR; Semi-parametri
 	-1 & 1 & 0 & 0 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Rho year fleet 1} \\
 	-1 & 1 & 0 & 0 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Rho age fleet 1} \\
 	\hline
-	\multicolumn{11}{l}{\# Additional fleets (e.g., fleet 2) with 2DAR selectivity}\\
-	\Tstrut &    &      &      &      & Sigma & Use & Len(1)/ &       & Before & After\\
-	Fleet & Ymin & Ymax & Amin & Amax & Amax  & Rho & Age(2)  & Phase & Range  & Range\Bstrut\\
+	\multicolumn{11}{l}{\# Additional fleets (e.g., fleet 2) with 2DAR selectivity} \\
+	\Tstrut &    &      &      &      & Sigma & Use & Len(1)/ &       & Before & After \\
+	Fleet & Ymin & Ymax & Amin & Amax & Amax  & Rho & Age(2)  & Phase & Range  & Range \Bstrut\\
 	\hline
-	2    & 1979 & 2015 &  2   &  10  & 1     & 1   & 2       & 5     & 0   & 0\Tstrut\\
+	2    & 1979 & 2015 &  2   &  10  & 1     & 1   & 2       & 5     & 0   & 0 \Tstrut\\
 		\hline
 	&    &      &       & PRIOR & PRIOR &       &     & & & \Tstrut\\
-	LO & HI & INIT & PRIOR & SD    & TYPE  & PHASE & \multicolumn{4}{l}{LABEL}\Bstrut\\
+	LO & HI & INIT & PRIOR & SD    & TYPE  & PHASE & \multicolumn{4}{l}{LABEL} \Bstrut\\
 	\hline
-	0 & 4 & 1 & 1 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Sigma selex fleet 1, first age}\Tstrut\\
-	0 & 4 & 1 & 1 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Sigma selex fleet 1, second age}\Tstrut\\
-	0 & 4 & 1 & 1 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Sigma selex fleet 1, ... age}\Tstrut\\
-	-1 & 1 & 0 & 0 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Rho year fleet 1}\\
+	0 & 4 & 1 & 1 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Sigma selex fleet 1, first age} \Tstrut\\
+	0 & 4 & 1 & 1 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Sigma selex fleet 1, second age} \Tstrut\\
+	0 & 4 & 1 & 1 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Sigma selex fleet 1, ... age} \Tstrut\\
+	-1 & 1 & 0 & 0 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Rho year fleet 1} \\
 	-1 & 1 & 0 & 0 & 0.1 & 6 & -4 & \multicolumn{4}{l}{\#Rho age fleet 1} \\
 	\hline
-	\multicolumn{11}{l}{\# Terminator line of 11 in length indicates the end of parameter input lines}\\
+	\multicolumn{11}{l}{\# Terminator line of 11 in length indicates the end of parameter input lines} \\
 	-9999 & 1 & 1 & 1 & 1 & 1 & 1 & 1 & 1 & 1 & 1 \\
 	\hline
 \end{longtable}
@@ -2409,36 +2409,36 @@ \subsection{Tag Recapture Parameters}
 Specify if tagging data are being used:
 
 
-\begin{longtable}{p{1cm} p{1cm} p{1cm}  p{1.5cm}  p{2.9cm}  p{1.25cm}  p{4.25cm} }
+\begin{longtable}{p{1cm} p{1cm} p{1cm} p{1.5cm} p{2.9cm} p{1.25cm} p{4.25cm}}
 	\hline
-	\multicolumn{3}{l}{Typical Value} &  \multicolumn{4}{l}{Description and Options}\Tstrut\Bstrut\\
+	\multicolumn{3}{l}{Typical Value} & \multicolumn{4}{l}{Description and Options} \Tstrut\Bstrut\\
 	\hline
-	\multicolumn{3}{l}{1} &  \multicolumn{4}{l}{Tagging Data Present:} \Tstrut\\
-	\multicolumn{3}{l}{}  &  \multicolumn{4}{l}{0 = No tagging data, or if tagging data is present in the data file, a value of 0} \\
-	\multicolumn{3}{l}{}  &  \multicolumn{4}{l}{ here will auto-generate the tag parameter section in the control.ss\_new file.}\\
-	\multicolumn{3}{l}{}  &  \multicolumn{4}{l}{1 = Read following lines of tagging data.} \Bstrut\\
+	\multicolumn{3}{l}{1} & \multicolumn{4}{l}{Tagging Data Present:} \Tstrut\\
+	\multicolumn{3}{l}{}  & \multicolumn{4}{l}{0 = No tagging data, or if tagging data is present in the data file, a value of 0} \\
+	\multicolumn{3}{l}{}  & \multicolumn{4}{l}{here will auto-generate the tag parameter section in the control.ss\_new file.} \\
+	\multicolumn{3}{l}{}  & \multicolumn{4}{l}{1 = Read following lines of tagging data.} \Bstrut\\
 
 
-	\multicolumn{7}{l}{COND = 1 Read the following long parameter lines:}\Tstrut\\
+	\multicolumn{7}{l}{COND = 1 Read the following long parameter lines:} \Tstrut\\
 	\hline
-	LO \Tstrut & HI & INIT & PRIOR &  <other entries> & Block Fxn & Parameter Label\Bstrut\\
+	LO \Tstrut & HI & INIT & PRIOR &  <other entries> & Block Fxn & Parameter Label \Bstrut\\
 	\hline
 	\endfirsthead
 
 	\hline
-	LO \Tstrut & HI & INIT & PRIOR & <other entries> & Block Fxn & Parameter Label\Bstrut\\
+	LO \Tstrut & HI & INIT & PRIOR & <other entries> & Block Fxn & Parameter Label \Bstrut\\
 	\hline
 	\endhead
 
 	\hline
 	\endfoot
 	\endlastfoot
 
-	-10 & 10 & 9 & 9 & \multicolumn{1}{c}{...} & 0 & \#TG loss init 1\Tstrut\\
-	-10 & 10 & 9 & 9 & \multicolumn{1}{c}{...} & 0 & \#TG loss chronic 1\\
-	  1 & 10 & 2 & 2 & \multicolumn{1}{c}{...} & 0 & \#TG loss overdispersion 1\\
-	-10 & 10 & 9 & 9 & \multicolumn{1}{c}{...} & 0 & \#TG report fleet 1\\
-	 -4 &  0 & 0 & 0 & \multicolumn{1}{c}{...} & 0 & \#TG report decay 1\Bstrut\\
+	-10 & 10 & 9 & 9 & \multicolumn{1}{c}{...} & 0 & \#TG loss init 1 \Tstrut\\
+	-10 & 10 & 9 & 9 & \multicolumn{1}{c}{...} & 0 & \#TG loss chronic 1 \\
+	  1 & 10 & 2 & 2 & \multicolumn{1}{c}{...} & 0 & \#TG loss overdispersion 1 \\
+	-10 & 10 & 9 & 9 & \multicolumn{1}{c}{...} & 0 & \#TG report fleet 1 \\
+	 -4 &  0 & 0 & 0 & \multicolumn{1}{c}{...} & 0 & \#TG report decay 1 \Bstrut\\
 	 \hline
 \end{longtable}
 
@@ -2463,11 +2463,11 @@ \subsection{Tag Recapture Parameters}
 A shortcoming was identified in the recapture calculations when using Pope's F Method and multiple seasons in SS3 prior to v.3.30.14. The internal calculations were corrected in v.3.30.14. Now the Z-at-age is applied internally for calculations of fishing pressure on the population when using the Pope calculations.
 
 \myparagraph{Mirroring of Tagging Parameters}
-In v.3.30.14, the ability to mirror the tagging parameters from another tag group or fleet was added. With this approach, the user can have just one parameter value for each of the five tagging parameter types and mirror all other parameters. Note that parameter lines are still required for the mirrored parameters and only lower numbered parameters can be mirrored. Mirroring is evoked through the phase input in the tagging parameter section.  The options are:
+In v.3.30.14, the ability to mirror the tagging parameters from another tag group or fleet was added. With this approach, the user can have just one parameter value for each of the five tagging parameter types and mirror all other parameters. Note that parameter lines are still required for the mirrored parameters and only lower numbered parameters can be mirrored. Mirroring is evoked through the phase input in the tagging parameter section. The options are:
 \begin{itemize}
 	\item No mirroring among tag groups or fleets: phase > -1000,
 	\item Mirror the next lower (i.e., already specified) tag group or fleet: phase = -1000 and set other parameter values the same as next lower Tag Group or fleet,
-	\item Mirror a lower (i.e., already specified) tag group of fleet x: phase = -100x and set other parameter values the same as the mirrored tag group or fleet( i.e., if you would like to mirror fleet 1 then the phase should -1001).
+	\item Mirror a lower (i.e., already specified) tag group of fleet x: phase = -100x and set other parameter values the same as the mirrored tag group or fleet (i.e., if you would like to mirror fleet 1 then the phase should -1001).
 \end{itemize}
 
 To avoid having to specify mirrored parameter lines, the tag parameters can be auto-generated. The control.ss\_new file created after running this model will have a full set of tagging parameter lines to use in future model runs.
@@ -2502,13 +2502,13 @@ \subsection{Variance Adjustment Factors}
 The input variance is in terms of the CV of the observation. Because such data are typically not very noisy, the variance adjustment is added to the CV and then multiplied by the observation to get the adjusted standard deviation of the observation.
 
 \myparagraph{Multiplicative Length Composition - Factor 4}
-The input variance is in terms of an effective sample size. The variance adjustment is multiplied times this sample size.  Set variance adjustment to 1.0 for no effect.
+The input variance is in terms of an effective sample size. The variance adjustment is multiplied times this sample size. Set variance adjustment to 1.0 for no effect.
 
 \myparagraph{Multiplicative Age Composition - Factor 5}
 Age composition is treated the same way as length composition.
 
 \myparagraph{Multiplicative Size-at-Age - Factor 6}	
-Size-at-age input variance is the sample size for the N observations at each age.  The variance adjustment is multiplied by these N values. Set to 1.0 for no effect.
+Size-at-age input variance is the sample size for the N observations at each age. The variance adjustment is multiplied by these N values. Set to 1.0 for no effect.
 
 \myparagraph{Multiplicative Generalized Size Composition - Factor 7}	
 Generalized size composition input variance is the sample size for each observation. The variance adjustment for each fleet is multiplied by these sample sizes. Set to 1.0 for no effect.
@@ -2526,12 +2526,12 @@ \subsection{Lambdas (Emphasis Factors)}
 
 \begin{tabular}{p{3cm} p{13cm}}
 	\hline
-	Typical Value & Description and Options\Tstrut\Bstrut\\
+	Typical Value & Description and Options \Tstrut\Bstrut\\
 	\hline
-	4 \Tstrut & Max lambda phase: read this number of lambda values for each element below.  The last lambda value is used for all higher numbered phases.\Bstrut\\
+	4 \Tstrut & Max lambda phase: read this number of lambda values for each element below. The last lambda value is used for all higher numbered phases. \Bstrut\\
 	1 & SD offset: \\
-	  & 0 = The ln(like) to omit the + ln(s) term,\\
-	  & 1 = The ln(like) to include the ln(s) term for CPUE, discard, growth CV, mean body weight, recruitment deviations. If you are estimating any variance parameters, SD offset must be set to 1.  \Bstrut\\
+	  & 0 = The ln(like) to omit the + ln(s) term, \\
+	  & 1 = The ln(like) to include the ln(s) term for CPUE, discard, growth CV, mean body weight, recruitment deviations. If you are estimating any variance parameters, SD offset must be set to 1. \Bstrut\\
 	\hline
 \end{tabular}
 
@@ -2540,9 +2540,9 @@ \subsection{Lambdas (Emphasis Factors)}
 \myparagraph{Lambda Usage Notes}
 \hypertarget{SaAlambda}{If} the CV for size-at-age is being estimated and the model contains mean size-at-age data, then the flag for inclusion of the + ln(stddev) term in the likelihood must be included. Otherwise, the model will always get a better fit to the mean size-at-age data by increasing the parameter for CV of size-at-age.
 
-The reading of the lambda values has been substantially altered with v.3.30. Instead of reading a matrix containing all the needed lambda values, the model now just reads those elements that will be given a value other than 1.0.  After reading the datafile, the model sets lambda equal to 0.0 if there are no data for a particular fleet/data type, and a value of 1.0 if data exist. So beware if your data files had data but you had set the lambda to 0.0 in a previous version of SS3.  First read an integer for the number of changes.
+The reading of the lambda values has been substantially altered with v.3.30. Instead of reading a matrix containing all the needed lambda values, the model now just reads those elements that will be given a value other than 1.0. After reading the datafile, the model sets lambda equal to 0.0 if there are no data for a particular fleet/data type, and a value of 1.0 if data exist. So beware if your data files had data but you had set the lambda to 0.0 in a previous version of SS3. First read an integer for the number of changes.
 
-You can put any placeholder value like 0 or 999 for fleet if the likelihood component is not fleet specific (like recdevs)
+You can put any placeholder value like 0 or 999 for fleet if the likelihood component is not fleet specific (like recdevs).
 
 You can also put any placeholder value like 0 or 999 for the SizeFreq Method unless the likelihood component you are changing the lambda for is 6 = size frequency, in which case you need to have a row for each size frequency method you want to modify and put the associated method number in that fourth column.
 
@@ -2555,16 +2555,17 @@ \subsection{Lambdas (Emphasis Factors)}
 	\hline
 	1 & 2 & 2 & 1.5 & 1 \Tstrut\\
 	4 & 2 & 2 & 10 & 1 \\
-	10 & 0 & 2 & ? & 0 \\
-	6 & ? & ? & ? & ? \\
+	10 & 0 & 2 & 1 & 0 \\ #not_fleet_specific
+	6 & 2 & 2 & 1.5 & 1 \\ #size_frequency_method_1
+	6 & 2 & 2 & 1 & 2 \\ #size_frequency_method_2
 	4 & 2 & 3 & 0.2 & 1 \\
 	-9999 & 1 & 1 & 1 & 1 \Bstrut\\
 	\hline
 \end{longtable}
 
 
 \begin{center}
-	\begin{longtable}{ p{7.5cm} p{7.5cm} }
+	\begin{longtable}{p{7.5cm} p{7.5cm}}
 		\multicolumn{2}{l}{The codes for component are:}\\
 		\hline
 		1 = survey  				   & 10 = recruitment deviations \Tstrut\\