Change PDF output template and fix preview images

.gitignore

@@ -5,3 +5,8 @@
 
 /.quarto/
 /_book/
+/site_libs/
+
+r4csr.tex
+index.adx
+index.thm

_quarto.yml

@@ -13,13 +13,15 @@ book:
  - Keaven Anderson
  - Yalin Zhu
  description: |
- This book will teach you how to prepare tables, listings, and figures for
+ Learn how to prepare tables, listings, and figures for
  clinical study report and submit to regulatory agencies,
  the essential part of clinical trial development.
 
- cover-image: "images/cover.png"
- image: "images/preview.png"
- favicon: "images/favicon.png"
+ output-file: "r4csr"
+
+ cover-image: "assets/cover.png"
+ image: "assets/preview.jpg"
+ favicon: "assets/favicon.png"
 
  site-url: https://r4csr.org/
  repo-url: https://github.com/elong0527/r4csr
@@ -28,13 +30,13 @@ book:
  reader-mode: true
 
  open-graph:
- image: https://r4csr.org/images/preview.jpg
+ image: assets/preview.jpg
  description: |
  Learn how to prepare tables, listings, and figures for
  clinical study report and submit to regulatory agencies,
  the essential part of clinical trial development.
  twitter-card:
- image: https://r4csr.org/images/preview.jpg
+ image: assets/preview.jpg
  description: |
  Learn how to prepare tables, listings, and figures for
  clinical study report and submit to regulatory agencies,
@@ -77,9 +79,15 @@ format:
  html:
  theme: [cosmo, custom.scss]
  mainfont: "Invention, system-ui, -apple-system, Segoe UI, Roboto, Helvetica Neue, Noto Sans, Liberation Sans, Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji, Segoe UI Symbol, Noto Color Emoji"
+ code-link: true
  pdf:
- documentclass: scrbook
- # Fixes 'Undefined control sequence \cellcolor' error
+ documentclass: tex/svmono
  include-in-header:
- - text: |
- \usepackage[table]{xcolor}
+ - "tex/preamble.tex"
+ include-before-body:
+ - "tex/before_body.tex"
+ include-after-body:
+ - "tex/after_body.tex"
+ cite-method: natbib
+ keep-tex: true
+ toc: true

index.qmd

@@ -1,5 +1,3 @@
-`r if (knitr::is_latex_output()) '<!--'`
-
 # Welcome {.unnumbered}
 
 Welcome to R for Clinical Study Reports and Submission.
@@ -16,6 +14,8 @@ clinical reporting toolkit.
 
 **This is a work-in-progress draft.**
 
+::: {.content-visible when-format="html"}
+
 ## Events {.unnumbered}
 
 ```{css, echo=FALSE}
@@ -34,9 +34,4 @@ knitr::kable(
 )
 ```
 
-## License {.unnumbered}
-
-This book is licensed to you under the
-[Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License](https://creativecommons.org/licenses/by-nc-nd/4.0/).
-
-`r if (knitr::is_latex_output()) '-->'`
+:::

tex/after_body.tex

@@ -0,0 +1,10 @@
+\backmatter
+
+\let\hyperlink=\oldhyperlink % Restore old hyperlink behaviour
+\cleardoublepage
+\markboth{Index}{Index}
+\addcontentsline{toc}{chapter}{Index}
+\printindex
+
+\addcontentsline{toc}{chapter}{Code index}
+\printindex[code]

tex/before_body.tex

@@ -0,0 +1,30 @@
+\null\vfill
+\begin{flushleft}
+\thispagestyle{empty}
+\textit{R for Clinical Study Reports and Submission}
+
+© Placeholder Name, Inc.
+
+ISBN-1234567891234
+
+\noindent Lorem ipsum dolor sit amet, consectetur adipiscing elit.
+Nulla et elementum libero. In hac habitasse platea dictumst.
+Vestibulum ante ipsum primis in faucibus orci luctus et ultrices
+posuere cubilia Curae; Donec sed odio dui. Nullam quis risus eget
+urna mollis ornare vel eu leo. Pellentesque habitant morbi tristique
+senectus et netus et malesuada fames ac turpis egestas.
+Curabitur blandit tempus porttitor.
+Integer posuere erat a ante venenatis dapibus posuere velit aliquet.
+\end{flushleft}
+
+\frontmatter
+
+% Dedication
+\begin{center}
+ \thispagestyle{empty}
+ \vspace*{\fill}
+ \huge{\textit{Placeholder for dedication text}}
+ \vspace*{\fill}
+\end{center}
+
+\mainmatter

tex/preamble.tex

@@ -0,0 +1,28 @@
+\usepackage{booktabs}
+
+\usepackage{float}
+\usepackage{index}
+% index functions separately
+\newindex{code}{adx}{and}{R code index}
+\newcommand{\indexf}[1]{\index[code]{#1@\texttt{#1()}}}
+\newcommand{\indexc}[1]{\index[code]{#1@\texttt{#1}}}
+
+\DeclareGraphicsExtensions{.pdf,.png}
+
+\usepackage{hyperref}
+% Place links in parens
+\renewcommand{\href}[2]{#2 (\url{#1})}
+% Use auto ref for internal links
+\let\oldhyperlink=\hyperlink
+\renewcommand{\hyperlink}[2]{\autoref{#1}}
+\def\chapterautorefname{Chapter}
+\def\sectionautorefname{Section}
+\def\subsectionautorefname{Section}
+\def\subsubsectionautorefname{Section}
+
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+\vbadness=10000 % suppress underfull \vbox
+\hbadness=10000 % suppress underfull \vbox
+\hfuzz=10pt
+
+\makeindex