The default template does produce the table of contents when reading in Acrobat. I'll see if I can produce a minimal example (it's currently 120 pages). FYI, here's the yaml header
---
title: "Graphical Analysis of Environmental Data using R"
mainfont: Calibri
sansfont: Calibri
monofont: Calibri
author: "David K Stevens"
date: "`r Sys.time()`"
site: bookdown::bookdown_site
lof: true
lot: true
includes: after_body
output:
bookdown::tufte_book2:
toc: true
keep_tex: true
includes:
before_body: frontpage.tex
after_body: after_body.tex
in_header: include_header.tex
tufte::tufte_book: default
tufte::tufte_handout: default
bookdown::gitbook: default
tufte::tufte_html: default
link-citations: yes
header-includes:
- \usepackage{leading}
- \leading{15pt}
- \usepackage{paralist}
- \let\itemize\compactitem
- \usepackage{titling}
- \pretitle{\begin{center}
\includegraphics[width=6in,height=9in]{cover.png}\LARGE\\}
- \posttitle{\end{center}}
- \usepackage{eso-pic,graphicx,transparent,comment}
- \usepackage[sfdefault]{roboto}
- \usepackage[T1]{fontenc}
- \usepackage{booktabs}
- \usepackage{longtable}
- \usepackage[most]{tcolorbox}
- \usepackage{multicol}
- \AtBeginEnvironment{tcolorbox}{\small}
documentclass: book
geometry: margin="left=1cm,right=1cm,top=1cm,bottom=1cm"
fontsize: 14pt
setmainfont: {Alegreya}
always_allow_html: yes
bibliography: DAB.bib
github-repo: rstudio/bookdown-demo
cover-image: "cover.png"
description: "This is a 1st attempt at a bookdown book on Environmental Data Analysis"
---