Change ss to ss3 in doc; also change gender to sex in tutorial (#198)

* change ss to ss3
* change gender to sex - stock-synthesis issue 516
* make all references to versions consistent
* note that SSI isn't maintained after v.3.30.21
* add info about @shcaba's tool
* add github discussions link

.github/workflows/deploy-ss3-docs.yml

@@ -37,8 +37,8 @@ jobs:
 
       - name: render the rmd files
         run: |
-          rmarkdown::render("User_Guides/ss_model_tips/ss_model_tips.Rmd", output_format = c("html_document", "pdf_document"), output_dir = "docs")
-          rmarkdown::render("User_Guides/getting_started/Getting_Started_SS.Rmd", output_format = c("html_document", "pdf_document"), output_dir = "docs")
+          rmarkdown::render("User_Guides/ss3_model_tips/ss3_model_tips.Rmd", output_format = c("html_document", "pdf_document"), output_dir = "docs")
+          rmarkdown::render("User_Guides/getting_started/Getting_Started_SS3.Rmd", output_format = c("html_document", "pdf_document"), output_dir = "docs")
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages

10optional_inputs.tex

@@ -2,17 +2,17 @@ \section{Optional Inputs}
 
 \hypertarget{WAA}{}
 \subsection{Empirical Weight-at-Age (wtatage.ss)}
-The model has the capability to read empirical body weight at age for the population and each fleet, in lieu of generating these weights internally from the growth parameters, weight-at-length, and size-selectivity.  Selection of this option is done by setting an explicit switch near the top of the control file.  The values are read from a separate file named, wtatage.ss.  This file is only required to exist if this option is selected.
+The model has the capability to read empirical body weight at age for the population and each fleet, in lieu of generating these weights internally from the growth parameters, weight-at-length, and size-selectivity. Selection of this option is done by setting an explicit switch near the top of the control file. The values are read from a separate file named, wtatage.ss. This file is only required to exist if this option is selected.
 
 The first value read is a single integer for the maximum age used in reading this file. So if the maximum age is 40, there will be 41 columns of weight-at-age entries to read, with the first column being for age 0. If the number of ages specified in this table is greater than maximum age in the model, the extra weight-at-age values are ignored. If the number of ages in this table is less than maximum age in the model, the weight-at-age data for the number of ages in the file is filled in for all unread ages out to maximum age.
 
 The format of this input file is:
 
-\begin{tabular}{l l l l l l l l l }
+\begin{tabular}{l l l l l l l l l}
 	\hline
-	40 & \multicolumn{8}{l}{Maximum Age}\\
+	40 & \multicolumn{8}{l}{Maximum Age} \\
 	\hline	
-	 &  &  & Growth & Birth & &  &  & \Tstrut\\
+	 &  &  & Growth & Birth &  &  &  & \Tstrut\\
 	Year & Season & Sex & Pattern & Season & Fleet & Age-0 & Age-1 & ... \Tstrut\Bstrut\\
 	\hline
 	\-1971 & 1 & 1 & 1 & 1 & -2 & 0      & 0      & 0.1003 \Tstrut\\
@@ -59,14 +59,14 @@ \subsection{Empirical Weight-at-Age (wtatage.ss)}
 
 
 \subsection{runnumber.ss}
-This file contains a single integer value.  It is read when the program starts, incremented by 1, used when processing the profile value inputs (see below), used as an identifier in the batch output, then saved with the incremented value.  Note that this incrementation may not occur if a run crashes.
+This file contains a single integer value. It is read when the program starts, incremented by 1, used when processing the profile value inputs (see below), used as an identifier in the batch output, then saved with the incremented value. Note that this incrementation may not occur if a run crashes.
 
 \subsection{profilevalues.ss}	
-This file contains information for changing the value of selected parameters for each run in a batch.  In the control file, each parameter that will be subject to modification by profilevalues.ss is designated by setting its phase to -9999.
+This file contains information for changing the value of selected parameters for each run in a batch. In the control file, each parameter that will be subject to modification by profilevalues.ss is designated by setting its phase to -9999.
 
-The first value in profilevalues.ss is the number of parameters to be batched.  This value MUST match the number of parameters with phase set equal to -9999 in the control file.  The program performs no checks for this equality.  If the value is zero in the first field, then nothing else will be read.  Otherwise, the model will read runnumber * Nparameters values and use the last Nparameters of these to replace the initial values of parameters designated with phase = --9999 in the control file.
+The first value in profilevalues.ss is the number of parameters to be batched. This value MUST match the number of parameters with phase set equal to -9999 in the control file. The program performs no checks for this equality. If the value is zero in the first field, then nothing else will be read. Otherwise, the model will read runnumber * Nparameters values and use the last Nparameters of these to replace the initial values of parameters designated with phase = --9999 in the control file.
 
-Usage Note: If one of the batch runs crashes before saving the updated value of runnumber.ss, then the processing of the profilevalue.ss will not proceed as expected.  Check the output carefully until a more robust procedure is developed. Also, this options was created before use of R became widespread.  You probably can create a more flexible approach using R today.
+Usage Note: If one of the batch runs crashes before saving the updated value of runnumber.ss, then the processing of the profilevalue.ss will not proceed as expected. Check the output carefully until a more robust procedure is developed. Also, this options was created before use of R became widespread. You probably can create a more flexible approach using R today.
 
 
 \pagebreak