Change org and repo names for migration to GHEC (#204)

* update org and repo names

.github/workflows/call-ss3-manual-html-release.yml

@@ -2,7 +2,7 @@ name: Build html for last release using texlive
 on: [workflow_dispatch]
 jobs:
   call-workflow:
-    uses: nmfs-stock-synthesis/doc/.github/workflows/build-ss3-manual-html.yml@main
+    uses: nmfs-ost/ss3-doc/.github/workflows/build-ss3-manual-html.yml@main
     with:
     # Note: upon new releases, will need to update this ref
       ref: 'v3.30.22'

.github/workflows/call-ss3-manual-pdf-release.yml

@@ -2,7 +2,7 @@ name: Build pdf for last release using texlive
 on: [workflow_dispatch]
 jobs:
   call-workflow:
-    uses: nmfs-stock-synthesis/doc/.github/workflows/build-ss3-manual-pdf.yml@main
+    uses: nmfs-ost/ss3-doc/.github/workflows/build-ss3-manual-pdf.yml@main
     with:
     # Note: upon new releases, will need to update this ref
       ref: 'v3.30.22'

12runningSS3.tex

@@ -253,7 +253,7 @@ \subsubsection{For Windows}
 To add the SS3 binary file to your path, follow these steps:
 
 \begin{enumerate}
-  \item Find the correct version of the SS3.exe binary on your computer (or download from the \href{https://github.com/nmfs-stock-synthesis/stock-synthesis/releases}{SS3 releases}).
+  \item Find the correct version of the SS3.exe binary on your computer (or download from the \href{https://github.com/nmfs-ost/ss3-source-code/releases}{SS3 releases}).
   \item Move to and note the folder location. E.g., \texttt{C:/SS3/}
   \item Click on the start menu and type \texttt{environment}
   \item Choose \texttt{Edit environment variables for your account} under Control Panel

1_4sections.tex

@@ -9,11 +9,11 @@ \section{Introduction}\label{sec:intro}
 
 Stock Synthesis is an age- and size-structured assessment model in the class of models termed integrated analysis models. Stock Synthesis has evolved since its initial inception in order to model a wide range of fish populations and dynamics.  The most recent major revision to Stock Synthesis occurred in 2016, when v.3.30 was introduced. This new version of Stock Synthesis required major revisions to the input files relative to earlier versions (see the \hypertarget{ConvIssues}{Converting Files} section for more information). The acronym for Stock Synthesis has evolved over time with earlier versions being referred to as SS2 (Stock Synthesis v.2.xx) and older versions as SS3 (Stock Synthesis v.3.xx). 
 
-SS3 has a population sub-model that simulates a stock's growth, maturity, fecundity, recruitment, movement, and mortality processes, an observation sub-model estimates expected values for various types of data, a statistical sub-model characterizes the data's goodness of fit and obtains best-fitting parameters with associated variance, and a forecast sub-model projects needed management quantities.  SS3 outputs the quantities, with confidence intervals, needed to implement risk-averse fishery control rules. The model is coded in C++ with parameter estimation enabled by automatic differentiation (\href{http://www.admb-project.org}{admb}). Windows, Linux, and iOS versions are available.  Output processing and associated tools are in R, and a graphical interface is in QT.  SS3 executables and support material is available on \href{https://github.com/nmfs-stock-synthesis}{GitHub}. The rich feature set in SS3 allows it to be configured for a wide range of situations.  SS3 has become the basis for a large fraction of U.S. assessments and many other assessments around the world.  
+SS3 has a population sub-model that simulates a stock's growth, maturity, fecundity, recruitment, movement, and mortality processes, an observation sub-model estimates expected values for various types of data, a statistical sub-model characterizes the data's goodness of fit and obtains best-fitting parameters with associated variance, and a forecast sub-model projects needed management quantities.  SS3 outputs the quantities, with confidence intervals, needed to implement risk-averse fishery control rules. The model is coded in C++ with parameter estimation enabled by automatic differentiation (\href{http://www.admb-project.org}{admb}). Windows, Linux, and iOS versions are available.  Output processing and associated tools are in R, and a graphical interface is in QT.  SS3 executables and support material is available on \href{https://github.com/nmfs-ost}{GitHub}. The rich feature set in SS3 allows it to be configured for a wide range of situations.  SS3 has become the basis for a large fraction of U.S. assessments and many other assessments around the world.  
 
-This manual provides a guide for using SS3. The guide contains a description of the input and output files and usage instructions. An overview and technical description of the model itself is in \citet{methotstock2013}. However, SS3 has continued to evolve and grow since the publication in 2013, with this manual reflecting the most up to date information regarding SS3.  The model and a graphical user interface are available on \href{https://github.com/nmfs-stock-synthesis}{GitHub} with older archived versions also available online at \href{https://vlab.noaa.gov/web/stock-synthesis}{NOAA VLAB}. The VLAB site also provides a user forum for posting questions and for accessing various additional materials. An output processor package, r4ss, in R is available for download from CRAN or \href{https://github.com/r4ss/r4ss}{GitHub}.
+This manual provides a guide for using SS3. The guide contains a description of the input and output files and usage instructions. An overview and technical description of the model itself is in \citet{methotstock2013}. However, SS3 has continued to evolve and grow since the publication in 2013, with this manual reflecting the most up to date information regarding SS3.  The model and a graphical user interface are available on \href{https://github.com/nmfs-ost}{GitHub} with older archived versions also available online at \href{https://vlab.noaa.gov/web/stock-synthesis}{NOAA VLAB}. The VLAB site also provides a user forum for posting questions and for accessing various additional materials. An output processor package, r4ss, in R is available for download from CRAN or \href{https://github.com/r4ss/r4ss}{GitHub}.
 
-Additional guidance for new users can be found online in the \href{https://nmfs-stock-synthesis.github.io/doc/Getting_Started_SS.html}{Getting Started Tutorial} and on the \href{https://github.com/nmfs-stock-synthesis/stock-synthesis#how-can-i-learn-how-to-use-stock-synthesis}{Stock Synthesis GitHub} page. 
+Additional guidance for new users can be found online in the \href{https://nmfs-ost.github.io/ss3-doc/Getting_Started_SS3.html}{Getting Started Tutorial} and on the \href{https://github.com/nmfs-ost/ss3-source-code#how-can-i-learn-how-to-use-stock-synthesis}{Stock Synthesis GitHub} page. 
 
   \subsection{How To Cite}
 

5converting.tex

@@ -1,6 +1,6 @@
 \hypertarget{ConvIssues}{}
 \section{Converting Files from Stock Synthesis v.3.24}
-Converting files from version 3.24 to version 3.30 can be performed by using the program ss\_trans.exe. This executable takes v.3.24 files as input and will output v.3.30 input and output files. SS\_trans executables are available for v.3.30.01 - v.3.30.17. The transitional executable was phased out with v.3.30.18. If a model needs to be converted from v.3.24 to a recent version, one should use the v.3.30.17 ss\_trans.exe available from the \href{https://github.com/nmfs-stock-synthesis/stock-synthesis/releases/tag/v3.30.17}{v.3.30.17 release page on GitHub} to convert the files and then any additional adjustments needed between v.3.30.17 and newer versions should be done by hand.
+Converting files from version 3.24 to version 3.30 can be performed by using the program ss\_trans.exe. This executable takes v.3.24 files as input and will output v.3.30 input and output files. SS\_trans executables are available for v.3.30.01 - v.3.30.17. The transitional executable was phased out with v.3.30.18. If a model needs to be converted from v.3.24 to a recent version, one should use the v.3.30.17 ss\_trans.exe available from the \href{https://github.com/nmfs-ost/ss3-source-code/releases/tag/v3.30.17}{v.3.30.17 release page on GitHub} to convert the files and then any additional adjustments needed between v.3.30.17 and newer versions should be done by hand.
 
 The following file structure and steps are recommended for converting model files:
 \begin{enumerate}

6starter.tex

@@ -98,6 +98,7 @@ \subsection{Starter File Options (starter.ss)}
    & & \\
    & & \\
    & & \\
+   & & \\
 
  \pagebreak
 %  \hline
@@ -207,8 +208,8 @@ \subsection{Starter File Options (starter.ss)}
    & 5 = unweighted average F for range of ages. & \\
    & & \\
    & & \\
-   & & \Bstrut\\
-   & & \Bstrut\\
+   & & \Bstrut\Bstrut\\
+   & & \Bstrut\Bstrut\\
    & & \Bstrut\\ 
   %  & & \\ 
 
@@ -236,6 +237,7 @@ \subsection{Starter File Options (starter.ss)}
   & 3 = make output subdirectory for each MCMC vector. & \Bstrut\\
   & & \Tstrut\Bstrut\\
   & & \\ 
+  & & \\ 
   % & & \\  		 
 
   \hline

8data.tex

@@ -863,7 +863,7 @@ \subsubsection{Ageing Error}
 
 The model is able to create one ageing error matrix from parameters, rather than from an input vector. The range of conditions in which this new feature will perform well has not been evaluated, so it should be considered as a preliminary implementation and subject to modification. To invoke this option, for the selected ageing error vector, set the standard deviation of ageing error to a negative value for age 0. This will cause creation of an ageing error matrix from parameters and any age or size-at-age data that specify use of this age error pattern will use this matrix. Then in the control file, add a full parameter line below the cohort growth deviation parameter (or the movement parameter lines if used) in the mortality growth parameter section. These parameters are described in the control file section of this manual.
 
-Code for ageing error calculation can be found in \href{https://github.com/nmfs-stock-synthesis/stock-synthesis/blob/main/SS_miscfxn.tpl}{SS\_miscfxn.tpl}, search for function ``get\_age\_age'' or ``SS\_Label\_Function 45''.
+Code for ageing error calculation can be found in \href{https://github.com/nmfs-ost/ss3-source-code/blob/main/SS_miscfxn.tpl}{SS\_miscfxn.tpl}, search for function ``get\_age\_age'' or ``SS\_Label\_Function 45''.
 
 \subsubsection{Age Composition Specification}
 If age data are included in the model, the following set-up is required, similar to the length data section.

9control.tex

@@ -745,7 +745,7 @@ \subsubsection{Ageing Error Parameters}
 	\item Power function coefficient for interpolating between those 2 values.
 \end{enumerate}
 
-\noindent Code for implementing vectors of mean age and standard deviation of age can be located online within the \href{https://github.com/nmfs-stock-synthesis/stock-synthesis/blob/main/SS_miscfxn.tpl}{SS\_miscfxn.tpl} file, search for function ``get\_age\_age'' or ``SS\_Label\_Function 45''.
+\noindent Code for implementing vectors of mean age and standard deviation of age can be located online within the \href{https://github.com/nmfs-ost/ss3-source-code/blob/main/SS_miscfxn.tpl}{SS\_miscfxn.tpl} file, search for function ``get\_age\_age'' or ``SS\_Label\_Function 45''.
 
 \subsubsection{Sex ratio}
 The last line in the mortality-growth parameter section allows the user to fix or estimate the sex ratio between female and male fish at recruitment. The parameter is specified in the fraction of female fish and is applied at settlement. The default option is a sex ratio of 0.50 with this parameter not being estimated. Any composition data input as type = 3, both sexes, will be informative to the sex ratio because it scales females and males together, not separately, for this data type input. Estimation of the sex ratio is a new feature and should be done with care with the user checking that the answer is reflective of the data.
@@ -1089,7 +1089,7 @@ \subsubsection{Spawner-Recruitment Functions}
 
 Unlike the Beverton-Holt stock-recruitment relationship, recruitment can increase above $R_0$ for stocks that are below $SB_0$ and thus the steepness is not fundamentally constrained below 1. However, in many cases, steepness will be limited well below 1 by the inequality above, which implies an inverse relationship between the maximum steepness and equilibrium survival. Specifically, the inequality above bounds steepness below 1 for all cases where $S_0$>0.2, which are those with the lowest fecundity, an intuitively reasonable result. For example, with $S_0$=0.4, the steepness is limited below 0.5, regardless of the choice of $z_{\text{frac}}$ or $\beta$. This natural limit on steepness may be one of the most valuable aspects of this stock-recruitment relationship.
 
-Code for the survival based recruitment can be found in \href{https://github.com/nmfs-stock-synthesis/stock-synthesis/blob/main/SS_recruit.tpl}{SS\_recruit.tpl}, search for ``SS\_Label\_43.3.7 survival based''.
+Code for the survival based recruitment can be found in \href{https://github.com/nmfs-ost/ss3-source-code/blob/main/SS_recruit.tpl}{SS\_recruit.tpl}, search for ``SS\_Label\_43.3.7 survival based''.
 
 \myparagraph{Shepherd}
 \hypertarget{Shepherd}{The} Shepherd stock recruit curve is calculated as:
@@ -1882,7 +1882,7 @@ \subsubsection{Selectivity Pattern Details}
 		\item To keep a constant rate of change in selectivity across a range of ages, use the -999 flag to keep the same rate of change in ln(selectivity) as for the previous age.
 	\end{itemize}
 
-Code for implementing random walk selectivity can be found in \href{https://github.com/nmfs-stock-synthesis/stock-synthesis/blob/main/SS_selex.tpl}{SS\_selex.tpl}, search for ``SS\_Label\_Info\_22.7.17''.
+Code for implementing random walk selectivity can be found in \href{https://github.com/nmfs-ost/ss3-source-code/blob/main/SS_selex.tpl}{SS\_selex.tpl}, search for ``SS\_Label\_Info\_22.7.17''.
 
 \myparagraph{Pattern 22 (size) - Double Normal with Plateau}
 	\begin{itemize}
@@ -2013,7 +2013,7 @@ \subsubsection{Selectivity Pattern Details}
 	\end{itemize}
 
 Code for implementing cubic spline selectivity can be found in
-\href{https://github.com/nmfs-stock-synthesis/stock-synthesis/blob/main/SS_selex.tpl}{SS\_selex.tpl},
+\href{https://github.com/nmfs-ost/ss3-source-code/blob/main/SS_selex.tpl}{SS\_selex.tpl},
 search for ``SS\_Label\_Info\_22.7.27''.
 
 One potential problem that may occur with a cubic spline is a U-shaped pattern in the selectivity around the first node. If this occurs, the initial set-up code (auto-generation options described below) can be changed from 0, 1 or 2 to 10, 11, or 12 which will cause selectivity to be fixed at 0.0 for all bins below the first node. A natural cubic spline (noted above) may be an alternative solution to this problem.

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing to doc
+# Contributing to ss3-doc
 
 ## General information
 Thank you for your interest in contributing to doc! We strive to follow the [NMFS Fisheries Toolbox Contribution Guide](https://github.com/nmfs-fish-tools/Resources/blob/master/CONTRIBUTING.md). Note that these are guidelines, not rules, and we are open to collaborations in other ways that may work better for you. Please feel free to reach out to us by opening an issue in this repository or by emailing the developers at [email protected].
@@ -7,6 +7,6 @@ This project and everyone participating in it is governed by the [NMFS Fisheries
 
 ## Compiling the Stock Synthesis manual
 
-The manual can be compiled locally using a [LaTeX compiler](https://www.overleaf.com/learn/latex/Choosing_a_LaTeX_Compiler), such as TexLive or MikTex. To compile the whole document, clone the repository and follow instructions for LaTeX compiling, applying them to [SS330_User_Manual.tex](https://github.com/nmfs-stock-synthesis/doc).
+The manual can be compiled locally using a [LaTeX compiler](https://www.overleaf.com/learn/latex/Choosing_a_LaTeX_Compiler), such as TexLive or MikTex. To compile the whole document, clone the repository and follow instructions for LaTeX compiling, applying them to [SS330_User_Manual.tex](https://github.com/nmfs-ost/ss3-doc).
 
-The manual is also compiled using github actions on every commit to the doc repository. The manual is saved as an artifact and is available for viewing. For those who don't want to compile locally, a pull request could be submitted with changes to the .tex files and github actions can be used to see the compiled products. The [call-ss3-manual-html job](https://github.com/nmfs-stock-synthesis/doc/blob/main/.github/workflows/call-ss3-manual-html.yml) compiles the html version of the manual (using pandoc and R code), while the [call-ss3-manual-pdf](https://github.com/nmfs-stock-synthesis/doc/blob/main/.github/workflows/call-ss3-manual-pdf.yml) job compiles the pdf version. call-ss3-manual-pdf-release.yml and call-ss3-manual-html-release.yml are only run manually (not with every commit).
+The manual is also compiled using github actions on every commit to the ss3-doc repository. The manual is saved as an artifact and is available for viewing. For those who don't want to compile locally, a pull request could be submitted with changes to the .tex files and github actions can be used to see the compiled products. The [call-ss3-manual-html job](https://github.com/nmfs-ost/ss3-doc/blob/main/.github/workflows/call-ss3-manual-html.yml) compiles the html version of the manual (using pandoc and R code), while the [call-ss3-manual-pdf](https://github.com/nmfs-ost/ss3-doc/blob/main/.github/workflows/call-ss3-manual-pdf.yml) job compiles the pdf version. call-ss3-manual-pdf-release.yml and call-ss3-manual-html-release.yml are only run manually (not with every commit).