note that SSI isn't maintained after v.3.30.21

12runningSS3.tex

@@ -284,11 +284,11 @@ \subsection{Running Stock Synthesis from R}
 
 Running SS3 from within R may be desirable for setting up simulations where many runs of SS3 models are required (e.g., \href{https://github.com/ss3sim/ss3sim}{ss3sim}) or if \texttt{r4ss} is already used to read model output.
 
-% \subsection{The Stock Synthesis GUI (SSI)}
-% \href{https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/5042951}{Stock Synthesis Interface} (SSI or the SS3 GUI) provides an interface for loading, editing, and running model files, and also can link to r4ss to generate plots.
+\subsection{The Stock Synthesis GUI (SSI)}
+\href{https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/5042951}{Stock Synthesis Interface} (SSI or the SS3 GUI) provides an interface for loading, editing, and running model files, and also can link to r4ss to generate plots. Note that SSI is not maintained for Stock Synthesis versions after v.3.30.21.
 
 \subsection{Debugging Tips}
-When input files are causing the program to crash or fail to produce sensible results, there are a few steps that can be taken to diagnose the problem.  Before trying the steps below, examine the echoinput.sso file.  It is highly annotated, so you should be able to see if the model is interpreting your input files as you intended.  Additionally, users should check the warning.sso file when attempting to debug a non-running model.
+When input files are causing the program to crash or fail to produce sensible results, there are a few steps that can be taken to diagnose the problem. Before trying the steps below, examine the echoinput.sso file.  It is highly annotated, so you should be able to see if the model is interpreting your input files as you intended.  Additionally, users should check the warning.sso file when attempting to debug a non-running model.
 
 \begin{enumerate}
 	\item Set the turn\_off\_phase switch to 0 in the starter.ss file.  This will cause the mode to not attempt to adjust any parameters and simply converges a dummy parameter.  It will still produce a Report.sso file, which can be examined to see what has been calculated from the initial parameter values.

User_Guides/getting_started/Getting_Started_SS3.Rmd

@@ -68,7 +68,7 @@ Many output text files are created during a model run. The most useful output fi
 
 + **r4ss**: An R package to plot SS3 model results and manipulate SS3 input and output files. Available at: https://github.com/r4ss/r4ss
 
-+ **SSI**: Stock Synthesis Interface (i.e., the SS3 GUI). The [latest version of SSI](https://github.com/nmfs-stock-synthesis/ssi/releases/latest) can be downloaded from GitHub. SSI can be used to edit, save, run, and visualize model inputs and outputs.
++ **SSI**: Stock Synthesis Interface (i.e., the SS3 GUI). The [latest version of SSI](https://github.com/nmfs-stock-synthesis/ssi/releases/latest) can be downloaded from GitHub. SSI can be used to edit, save, run, and visualize model inputs and outputs. Note that SSI is not maintained for Stock Synthesis versions after v.3.30.21.
 
 # Running SS3
 

User_Guides/ss3_model_tips/ss3_model_tips.Rmd

@@ -37,7 +37,7 @@ There are many potential workflows for developing a new SS3 model, but a common
 
 Some commonly used tools for editing the SS3 input files are:
 
-1. [**Stock Synthesis Interface (SSI; the SS3 GUI)**](https://github.com/nmfs-stock-synthesis/ssi). The SSI allows you to read in a model, performs some checks to ensure valid inputs, make modifications to the model, and offers visualizations of inputs. You can also run models from SSI.
+1. [**Stock Synthesis Interface (SSI; the SS3 GUI)**](https://github.com/nmfs-stock-synthesis/ssi). The SSI allows you to read in a model, performs some checks to ensure valid inputs, make modifications to the model, and offers visualizations of inputs. You can also run models from SSI. Note that SSI is not maintained for Stock Synthesis versions after v.3.30.21.
 2. **Your favorite text editor**.
 3. **The ```SS_read*``` and ```SS_write*``` functions in the R package [r4ss](https://github.com/r4ss/r4ss)**. These functions allow you to read in SS3 input files to R, manipulate them from within R, then write them out to a file. The [r4ss vignette](https://r4ss.github.io/r4ss/vignettes/r4ss-intro-vignette.html#scripting-stock-synthesis-workflows-with-r4ss) demonstrates how to use these functions