Adding sections to ms and switching to APA refs.

Adding data accessiblity and author contributions sections. Swithing to
APA-formatted citations and bibliography. Reformatting for submission.

tex/manuscript/author-contributions.tex

@@ -0,0 +1,6 @@
+J.R.O.\ conceived the study.
+J.R.O.\ and N.L.\ designed and executed the simulation analyses.
+K.A.C.\ assembled the stickleback sequence data, and
+J.R.O.\ and K.A.C.\ analyzed those data.
+J.R.O.\ led the writing of the manuscript, with contributions from N.L.\ and
+K.A.C.

tex/manuscript/data-accessibility.tex

@@ -0,0 +1,5 @@
+A detailed history of all aspects of this project was recorded in a
+version-controlled repository, which is publicly available at
+\url{https://github.com/phyletica/ecoevolity-demog-experiments},
+and was archived on zenodo
+(\url{https://dx.doi.org/XXXXXXX}).

tex/manuscript/main.tex

@@ -9,16 +9,17 @@
 \input{../utils/macros.tex}
 \input{../utils/notation.tex}
 
-\newcommand{\ifembed}[2]{#1}
-% \newcommand{\ifembed}[2]{#2}
-% \newcommand{\ifdoublespacing}[2]{#1}
-\newcommand{\ifdoublespacing}[2]{#2}
-% \newcommand{\iflinenumbers}[2]{#1}
-\newcommand{\iflinenumbers}[2]{#2}
+% \newcommand{\ifembed}[2]{#1}
+\newcommand{\ifembed}[2]{#2}
+\newcommand{\ifdoublespacing}[2]{#1}
+% \newcommand{\ifdoublespacing}[2]{#2}
+\newcommand{\iflinenumbers}[2]{#1}
+% \newcommand{\iflinenumbers}[2]{#2}
 % \newcommand{\ifragged}[2]{#1}
 \newcommand{\ifragged}[2]{#2}
 
-\usepackage[round]{natbib}
+% \usepackage[round]{natbib}
+\usepackage[natbibapa]{apacite}
 
 \title{Insights from a general, full-likelihood Bayesian approach to inferring
     shared evolutionary events from genomic data: Inferring shared demographic
@@ -58,7 +59,7 @@
 \begin{linenumbers}
 }{}
 
-% \textbf{Running head}: \uppercase{Inferring shared demographic changes}
+\textbf{Running head}: \uppercase{Inferring shared demographic changes}
 
 {\let\newpage\relax\maketitle}
 
@@ -79,18 +80,28 @@
 
 \input{body.tex}
 
+
 \section{Acknowledgments}
 \input{acknowledgments.tex}
 
+% \bibliographystyle{../bib/sysbio}
+\bibliographystyle{apacite}
+\bibliography{../bib/references}
+
+\section{Data Accessibility}
+\input{data-accessibility.tex}
+
+\section{Author Contributions}
+\input{author-contributions.tex}
+
 % \section{Appendix}
 \begin{appendices}
 \section{The full model}
 \label{appendix:model}
 \input{model.tex}
 \end{appendices}
 
-\bibliographystyle{../bib/sysbio}
-\bibliography{../bib/references}
+%TC:ignore
 
 %% LIST OF FIGURES %%%%%%%%%%%%%%%%%%%%%%%%%%
 % \ifembed{}{
@@ -155,4 +166,6 @@ \section*{Supporting Information}
 
 \input{si-figures.tex}
 
+%TC:endignore
+
 \end{document}

tex/utils/preamble.tex

@@ -44,8 +44,8 @@
 
 \usepackage{hyperref}
 \hypersetup{pdfborder={0 0 0},
-            colorlinks=true,
-            % colorlinks=false,
+            % colorlinks=true,
+            colorlinks=false,
             urlcolor=porange,
             linkcolor=pauburn,
             citecolor=pteal}