feat: formatting for PCI_Archaeo

analysis/paper/_quarto.yml

@@ -43,26 +43,26 @@ title-block-published: "Last updated"
 format:
   html:
     theme: cosmo
-    output-file: "preprint-for-PCI_v2.html"
+    output-file: "preprint-for-PCI_v3.html"
     keep-md: true
   pdf:
     keep-tex: true
-    output-file: "preprint-for-PCI_v2.pdf"
+    output-file: "preprint-for-PCI_v3.pdf"
     documentclass: article
+    number-sections: true
     geometry:
-      - top=30mm
+      - top=10mm
+      - bottom=10mm
       - left=30mm
       - heightrounded
     include-in-header:
-      text: |
-        \usepackage{lineno}
+      file: ../templates/_preface.tex
     template-partials:
       - ../templates/_authors.tex
       - ../templates/_affiliations.tex
       - ../templates/before-body.tex
   docx:
     output-file: "draft-manuscript-3.docx"
-#output-file: "_output/draft-manuscript-2"
 execute:
   freeze: auto
   echo: false
@@ -73,10 +73,6 @@ knitr:
     comment: "#>"
     fig-path: "../figures/"
     fig-dpi: 600
-# filters:
-#   - ../templates/scholarly-metadata.lua
-#   - ../templates/author-info-blocks.lua
-#   - ../templates/pagebreak.lua
 bibliography: references.bib
 csl: "apa.csl" # Insert path for the bib-style
 abstract: |

analysis/paper/paper.qmd

@@ -50,10 +50,16 @@ Louise Le Meillour for taking on our preprint and providing helpful comments,
 and Mario Zimmerman and two other anonymous reviewers for their time and invaluable
 insights.
 
+## Funding {-}
+
 This research has received funding from the European Research Council under the
 European Union’s Horizon 2020 research and innovation program, grant agreement
 number STG–677576 (“HARVEST”).
 
+## Conflict of interest disclosure {-}
+
+The authors have no conflicts to declare.
+
 ## Data Availability Statement {-}
 
 All raw data is available on Zenodo (<https://doi.org/10.5281/zenodo.8061483>).
@@ -62,9 +68,6 @@ supplementary materials are available as a research compendium
 (<https://doi.org/10.5281/zenodo.7649825>)
 using the structure recommended by the **rrtools** R package [@Rrrtools].
 
-## Conflict of interest disclosure {-}
-
-The authors have no conflicts to declare.
 
 ## References {-}
 

analysis/paper/paper.tex

@@ -38,9 +38,9 @@
   \KOMAoptions{parskip=half}}
 \makeatother
 \usepackage{xcolor}
-\usepackage[top=30mm,left=30mm,heightrounded]{geometry}
+\usepackage[top=10mm,bottom=10mm,left=30mm,heightrounded]{geometry}
 \setlength{\emergencystretch}{3em} % prevent overfull lines
-\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
+\setcounter{secnumdepth}{5}
 % Make \paragraph and \subparagraph free-standing
 \ifx\paragraph\undefined\else
   \let\oldparagraph\paragraph
@@ -114,7 +114,26 @@
 \usepackage[normalem]{ulem}
 \usepackage{makecell}
 \usepackage{xcolor}
-\usepackage{lineno}
+\usepackage{fancyhdr, graphicx}
+\usepackage[hidelinks]{hyperref}
+
+\fancyhead{\vspace{70pt}}
+\renewcommand{\headrulewidth}{1.8pt}
+
+\makeatletter
+\def\@maketitle{%
+  \newpage
+  \hfill\href{https://doi.org/10.24072/pci.archaeo.100389}{\includegraphics[width=3.5cm]{badge_PCI_Archaeology.png}}\hfill
+  \null
+ \begin{center}
+{\LARGE
+\textbf\newline{\@title}
+}
+%\newline
+
+\end{center}
+  \par}
+\makeatother
 \makeatletter
 \makeatother
 \makeatletter
@@ -196,15 +215,13 @@
 
 \begin{document}
 %% modified from: https://github.com/quarto-journals/plos/blob/main/_extensions/plos/partials/before-body.tex
-\begin{flushleft}
-{\LARGE
-\textbf\newline{Multiproxy analysis exploring patterns of diet and
-disease in dental calculus and skeletal remains from a 19th century
-Dutch population}
-}
-\newline
 
-\vspace{12pt}
+\maketitle
+
+\begin{center}
+
+\thispagestyle{fancy}
+
 % Insert author names, affiliations and corresponding author email
 
 \normalsize{Bjørn Peare
@@ -214,20 +231,23 @@
 Casna}\textsuperscript{1}, \normalsize{Menno
 Hoogland}\textsuperscript{1}, \normalsize{Historisch Genootschap
 Beemster}\textsuperscript{3}, \normalsize{Amanda G.
-Henry}\textsuperscript{1}
-\\
-\bigskip
-\small{1} \small{Department of Archaeological Sciences, Leiden
-University}\\ \small{2} \small{Department of Forensic Medicine, Aarhus
-University}\\ \small{3} \small{Historisch Genootschap Beemster}
-\newline
+Henry}\textsuperscript{1}\vspace{12pt}
 
-% Use the asterisk to denote corresponding authorship and provide email address in note below.
-* [email protected]
+\rule{\textwidth}{1.8pt}\vspace{8pt}
 
-\end{flushleft}
+\end{center}
 
-\linenumbers
+\textsuperscript{\footnotesize{1}}\textit{\small{Department of
+Archaeological Sciences, Leiden
+University}}\\ \textsuperscript{\footnotesize{2}}\textit{\small{Department
+of Forensic Medicine, Aarhus
+University}}\\ \textsuperscript{\footnotesize{3}}\textit{\small{Historisch
+Genootschap Beemster}}
+
+% Use the asterisk to denote corresponding authorship and provide email address in note below.
+* \small{[email protected]}
+
+\vspace{12pt}
 
 \begin{abstract}
 Dental calculus is an excellent source of information on the dietary
@@ -270,12 +290,15 @@
 children and women.
 \end{abstract}
 
-Keywords:  dental calculus; LC-MS/MS; alkaloids; dental pathology;
-sinusitis; caffeine; tobacco 
-\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[borderline west={3pt}{0pt}{shadecolor}, interior hidden, enhanced, boxrule=0pt, sharp corners, breakable, frame hidden]}{\end{tcolorbox}}\fi
+\small \textbf{Keywords:}  dental calculus; LC-MS/MS; alkaloids; dental
+pathology; sinusitis; caffeine; tobacco   \\
+
+\vfill
+
+\newgeometry{top=30mm,left=30mm}\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[breakable, interior hidden, borderline west={3pt}{0pt}{shadecolor}, enhanced, boxrule=0pt, sharp corners, frame hidden]}{\end{tcolorbox}}\fi
 
 \hypertarget{introduction}{%
-\subsection{Introduction}\label{introduction}}
+\section{Introduction}\label{introduction}}
 
 Dental calculus has proven to be an excellent source of a wide variety
 of information about our past. The increased accessibility and
@@ -346,7 +369,7 @@ \subsection{Introduction}\label{introduction}}
 identification of pipe notches in the dentition.
 
 \hypertarget{materials}{%
-\subsection{Materials}\label{materials}}
+\section{Materials}\label{materials}}
 
 The sample consists of 41 individuals from Middenbeemster, a 19th
 century rural Dutch site. The village of Middenbeemster and the
@@ -390,10 +413,10 @@ \subsection{Materials}\label{materials}}
 \end{figure}
 
 \hypertarget{methods}{%
-\subsection{Methods}\label{methods}}
+\section{Methods}\label{methods}}
 
 \hypertarget{skeletal-analysis}{%
-\subsubsection{Skeletal analysis}\label{skeletal-analysis}}
+\subsection{Skeletal analysis}\label{skeletal-analysis}}
 
 Demographic and pathological analyses were conducted in the Laboratory
 for Human Osteoarchaeology at Leiden University. Sex was estimated using
@@ -409,7 +432,7 @@ \subsubsection{Skeletal analysis}\label{skeletal-analysis}}
 bones and the extent of taphonomic degradation.
 
 \hypertarget{paleopathology}{%
-\paragraph{Paleopathology}\label{paleopathology}}
+\subsubsection{Paleopathology}\label{paleopathology}}
 
 Pathological conditions and lesions that occur frequently in the
 population were included in the analysis. Data were dichotomised to
@@ -435,7 +458,7 @@ \subsubsection{Skeletal analysis}\label{skeletal-analysis}}
 associated pitting.
 
 \hypertarget{dental-pathology}{%
-\paragraph{Dental pathology}\label{dental-pathology}}
+\subsubsection{Dental pathology}\label{dental-pathology}}
 
 Caries ratios were calculated by dividing the number of lesions by the
 number of teeth scored, resulting in a single caries ratio per
@@ -457,7 +480,7 @@ \subsubsection{Skeletal analysis}\label{skeletal-analysis}}
 of each tooth to alveolar bone (Maat \& Mastwijk, 2005).
 
 \hypertarget{calculus-sampling}{%
-\subsubsection{Calculus sampling}\label{calculus-sampling}}
+\subsection{Calculus sampling}\label{calculus-sampling}}
 
 Where possible, we used material that had already been sampled for a
 previous study to prevent unnecessary repeated sampling of individuals.
@@ -479,7 +502,7 @@ \subsubsection{Calculus sampling}\label{calculus-sampling}}
 chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis.
 
 \hypertarget{uhplc-msms}{%
-\subsubsection{UHPLC-MS/MS}\label{uhplc-msms}}
+\subsection{UHPLC-MS/MS}\label{uhplc-msms}}
 
 The list of targeted compounds included both naturally occurring
 compounds known to have been used in the past, as well as synthetic
@@ -504,7 +527,7 @@ \subsubsection{UHPLC-MS/MS}\label{uhplc-msms}}
 validation, see the original study by Sørensen and colleagues (2021).
 
 \hypertarget{statistical-analysis}{%
-\subsubsection{Statistical analysis}\label{statistical-analysis}}
+\subsection{Statistical analysis}\label{statistical-analysis}}
 
 All compounds and pathological conditions/lesions were converted to a
 presence/absence score. Pearson product-moment correlation was applied
@@ -524,7 +547,7 @@ \subsubsection{Statistical analysis}\label{statistical-analysis}}
 were calculated with the \textbf{psych} package (Revelle, 2022).
 
 \hypertarget{results}{%
-\subsection{Results}\label{results}}
+\section{Results}\label{results}}
 
 Multiple compounds were detected in the dental calculus samples.
 Compounds detected at a lower concentration than the lower limit of
@@ -636,7 +659,7 @@ \subsection{Results}\label{results}}
 nicotine and cotinine, and had no signs of a pipe notch.
 
 \hypertarget{correlations-between-detected-alkaloids-and-diseases}{%
-\subsubsection{Correlations between detected alkaloids and
+\subsection{Correlations between detected alkaloids and
 diseases}\label{correlations-between-detected-alkaloids-and-diseases}}
 
 For further statistical analyses, only the UHPLC-MS/MS results from
@@ -761,7 +784,7 @@ \subsubsection{Correlations between detected alkaloids and
 \end{figure}
 
 \hypertarget{discussion}{%
-\subsection{Discussion}\label{discussion}}
+\section{Discussion}\label{discussion}}
 
 In this study we were able to extract and identify multiple alkaloids
 and salicylic acid from the dental calculus of individuals from
@@ -1042,7 +1065,7 @@ \subsection{Discussion}\label{discussion}}
 pathways of dietary (and other) compounds.
 
 \hypertarget{conclusions}{%
-\subsection{Conclusions}\label{conclusions}}
+\section{Conclusions}\label{conclusions}}
 
 This preliminary study outlines the benefits of using calculus to target
 a variety of compounds that could have been consumed as medicine or
@@ -1064,8 +1087,8 @@ \subsection{Conclusions}\label{conclusions}}
 whether dietary, medicinal, recreational, or otherwise.
 
 \hypertarget{acknowledgements}{%
-\subsection*{Acknowledgements}\label{acknowledgements}}
-\addcontentsline{toc}{subsection}{Acknowledgements}
+\section*{Acknowledgements}\label{acknowledgements}}
+\addcontentsline{toc}{section}{Acknowledgements}
 
 We wish to thank Kirsten Ziesemer for helping track down the calculus
 samples from her studies. Additionally, we owe special thanks to Vincent
@@ -1075,14 +1098,25 @@ \subsection*{Acknowledgements}\label{acknowledgements}}
 preprint and providing helpful comments, and Mario Zimmerman and two
 other anonymous reviewers for their time and invaluable insights.
 
+\hypertarget{funding}{%
+\section*{Funding}\label{funding}}
+\addcontentsline{toc}{section}{Funding}
+
 This research has received funding from the European Research Council
 under the European Union's Horizon 2020 research and innovation program,
 grant agreement number STG--677576 (``HARVEST'').
 
+\hypertarget{conflict-of-interest-disclosure}{%
+\section*{Conflict of interest
+disclosure}\label{conflict-of-interest-disclosure}}
+\addcontentsline{toc}{section}{Conflict of interest disclosure}
+
+The authors have no conflicts to declare.
+
 \hypertarget{data-availability-statement}{%
-\subsection*{Data Availability
+\section*{Data Availability
 Statement}\label{data-availability-statement}}
-\addcontentsline{toc}{subsection}{Data Availability Statement}
+\addcontentsline{toc}{section}{Data Availability Statement}
 
 All raw data is available on Zenodo
 (\url{https://doi.org/10.5281/zenodo.8061483}). Analysis scripts, and
@@ -1091,16 +1125,9 @@ \subsection*{Data Availability
 (\url{https://doi.org/10.5281/zenodo.7649825}) using the structure
 recommended by the \textbf{rrtools} R package (Marwick, 2019).
 
-\hypertarget{conflict-of-interest-disclosure}{%
-\subsection*{Conflict of interest
-disclosure}\label{conflict-of-interest-disclosure}}
-\addcontentsline{toc}{subsection}{Conflict of interest disclosure}
-
-The authors have no conflicts to declare.
-
 \hypertarget{references}{%
-\subsection*{References}\label{references}}
-\addcontentsline{toc}{subsection}{References}
+\section*{References}\label{references}}
+\addcontentsline{toc}{section}{References}
 
 \hypertarget{refs}{}
 \begin{CSLReferences}{1}{0}

analysis/templates/_affiliations.tex

@@ -1 +1 @@
-\small{$it.number$} $if(it.name)$\small{$it.name$}$endif$
+\textsuperscript{\footnotesize{$it.number$}}$if(it.name)$\textit{\small{$it.name$}}$endif$

analysis/templates/_preface.tex

@@ -0,0 +1,20 @@
+\usepackage{fancyhdr, graphicx}
+\usepackage[hidelinks]{hyperref}
+
+\fancyhead{\vspace{70pt}}
+\renewcommand{\headrulewidth}{1.8pt}
+
+\makeatletter
+\def\@maketitle{%
+  \newpage
+  \hfill\href{https://doi.org/10.24072/pci.archaeo.100389}{\includegraphics[width=3.5cm]{badge_PCI_Archaeology.png}}\hfill
+  \null
+ \begin{center}
+{\LARGE
+\textbf\newline{\@title}
+}
+%\newline
+
+\end{center}
+  \par}
+\makeatother