runningSS to runningSS3

13output.tex

@@ -45,7 +45,7 @@ \subsection{Custom Reporting}
 \subsection{Standard ADMB output files}
 Standard ADMB files are created by SS3. These are:
 
-ss.par - This file has the final parameter values. They are listed in the order they are declared in SS3. This file can be read back into SS3 to restart a run with these values (see \hyperref[sec:RunningSS]{Running Stock Synthesis} for more info).
+ss.par - This file has the final parameter values. They are listed in the order they are declared in SS3. This file can be read back into SS3 to restart a run with these values (see \hyperref[sec:RunningSS3]{Running Stock Synthesis} for more info).
 
 ss.std - This file has the parameter values and their estimated standard deviation for those parameters that were active during the model run. It also contains the derived quantities declared as standard deviation report variables. All of this information is also report in the covar.sso. Also, the parameter section of Report.sso lists all the parameters with their SS3 generated names, denotes which were active in the reported run, displays the parameter standard deviations, then displays the derived quantities with their standard deviations.
 

1_4sections.tex

@@ -71,7 +71,7 @@ \section{File Organization}\label{FileOrganization}
 \pagebreak
 
 \section{Starting Stock Synthesis}
-SS3 is typically run through the command line interface, although it can also be called from another program, R, the Stock Synthesis Interface, or a script file (such as a DOS batch file). SS3 is compiled for Windows, Mac, and Linux operating systems. The memory requirements depend on the complexity of the model you run, but in general, SS3 will run much slower on computers with inadequate memory. See \hyperref[sec:RunningSS]{Running Stock Synthesis} for additional notes on methods of running SS3.
+SS3 is typically run through the command line interface, although it can also be called from another program, R, the Stock Synthesis Interface, or a script file (such as a DOS batch file). SS3 is compiled for Windows, Mac, and Linux operating systems. The memory requirements depend on the complexity of the model you run, but in general, SS3 will run much slower on computers with inadequate memory. See \hyperref[sec:RunningSS3]{Running Stock Synthesis} for additional notes on methods of running SS3.
 
 Communication with the program is through text files. When the program first starts, it reads the file starter.ss, which typically must be located in the same directory from which SS3 is being run. The file starter.ss contains required input information plus references to other required input files, as described in the \hyperref[FileOrganization]{File Organization section}. The names of the control and data files must match the names specified in the starter.ss file. File names, including starter.ss, are case-sensitive on Linux and Mac systems but not on Windows. The echoinput.sso file outputs how the executable reads each input file and can be used for troubleshooting when trying to setup a model correctly. Output from SS3 consists of text files containing specific keywords. Output processing programs, such as Excel, or R can search for these keywords and parse the specific information located below that keyword in the text file.
 

SS330_User_Manual.tex

@@ -199,7 +199,7 @@
 	% ======== Section 11: Likelihoods
 	\input{11likelihoods}
 	%========= Section 12: Running SS
-	\input{12runningSS}	
+	\input{12runningSS3}	
 	% ======== Section 13: Output Files
 	\input{13output}	
 	%========= Section 14: R4SS

User_Guides/getting_started/Getting_Started_SS3.Rmd

@@ -72,7 +72,7 @@ Many output text files are created during a model run. The most useful output fi
 
 # Running SS3
 
-SS3 is typically run through the command line (although it can also be run indirctly via the commandline through an R console). We will introduce the one folder approach, where SS3 is in the same folder as the model files. Other possible approaches to running SS3 include, which are detailed in the ["Running Stock Synthesis" section of the user manual](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#sec:RunningSS).
+SS3 is typically run through the command line (although it can also be run indirctly via the commandline through an R console). We will introduce the one folder approach, where SS3 is in the same folder as the model files. Other possible approaches to running SS3 include, which are detailed in the ["Running Stock Synthesis" section of the user manual](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#sec:RunningSS3).
 
 ## The one folder approach and demonstration of an SS3 model run
 
@@ -174,7 +174,7 @@ Here are some basic checks for when SS3 does not run:
  + Check that starter.ss references the correct names of the control and data files.
  + If SS3 starts to read files and then crashes, check warnings.sso and echoinput.sso. The warnings.sso will reveal potential issues with the model, while echoinput.sso will show how far SS3 was able to run. Work backwards from the bottom of echoinput.sso, looking for where SS3 stopped and if the inputs are being read corectly or not.
 
-For further information on troubleshooting, please refer to the SS3 User Manual [“Running Stock Synthesis” subsections](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#sec:RunningSS), especially [“Re-Starting a Run”](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#re-starting-a-run) and  [“Debugging Tips”](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#debugging-tips).
+For further information on troubleshooting, please refer to the SS3 User Manual [“Running Stock Synthesis” subsections](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#sec:RunningSS3), especially [“Re-Starting a Run”](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#re-starting-a-run) and  [“Debugging Tips”](https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#debugging-tips).
 
 # Where to get additional help