diff --git a/tex/manuscript/author-contributions.tex b/tex/manuscript/author-contributions.tex new file mode 100644 index 0000000..3552b6b --- /dev/null +++ b/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. diff --git a/tex/manuscript/data-accessibility.tex b/tex/manuscript/data-accessibility.tex new file mode 100644 index 0000000..346038e --- /dev/null +++ b/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}). diff --git a/tex/manuscript/main.tex b/tex/manuscript/main.tex index 507161c..ec59111 100644 --- a/tex/manuscript/main.tex +++ b/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} @@ -79,9 +80,20 @@ \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} @@ -89,8 +101,7 @@ \section{The full 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} diff --git a/tex/utils/preamble.tex b/tex/utils/preamble.tex index 31634ee..b105ec4 100644 --- a/tex/utils/preamble.tex +++ b/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}