here is the minimal example

01-intro.Rmd

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+# Introduction {#intro}
+
+You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \@ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \@ref(methods).
+
+Figures and tables with captions will be placed in `figure` and `table` environments, respectively.
+
+```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'}
+par(mar = c(4, 4, .1, .1))
+plot(pressure, type = 'b', pch = 19)
+```
+
+Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table \@ref(tab:nice-tab).
+
+```{r nice-tab}
+knitr::kable(head(iris, 20), caption = 'Here is a nice table!', booktabs = TRUE)
+```
+
+You can write citations, too. For example, we are using the **bookdown** package [@R-bookdown] in this sample book, which was built on top of R Markdown and **knitr** [@xie2015].

02-literature.Rmd

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+# Literature
+
+Here is a review of existing methods.

03-method.Rmd

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+# Methods
+
+We describe our methods in this chapter.

04-application.Rmd

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+# Applications
+
+Some _significant_ applications are demonstrated in this chapter.
+
+## Example one
+
+## Example two

05-summary.Rmd

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+# Final Words
+
+We have finished a nice book.

06-references.Rmd

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+`r if (knitr:::is_html_output()) '# References'`
+
+```{r include=FALSE}
+# automatically create a bib database for R packages
+knitr::write_bib(c(
+  .packages(), 'bookdown', 'knitr', 'rmarkdown'
+), 'packages.bib')
+```
+

Makefile

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+RMD_FILES := $(filter-out _%, $(wildcard *.Rmd))
+HTML_FILES := $(patsubst %.Rmd, %.html, $(RMD_FILES))
+
+all: $(HTML_FILES)
+
+%.html: %.Rmd
+	Rscript -e "bookdown::render_book('$<', 'bookdown::html_chapters')"
+
+pdf: book.pdf
+
+%.pdf: %.Rmd $(RMD_FILES)
+	Rscript -e "bookdown::render_book('$<', 'bookdown::pdf_book')"

_config.yml

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+main_rmd: "book.Rmd"
+chapter_name: "CHAPTER "

book.bib

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+@Book{xie2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {http://yihui.name/knitr/},
+}

bookdown-demo.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes

index.Rmd

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+--- 
+title: "A Minimal Book Example"
+author: "Yihui Xie"
+date: "`r Sys.Date()`"
+knit: "bookdown::render_book"
+output:
+  bookdown::html_chapters:
+    css: style.css
+    md_extensions: +markdown_in_html_blocks
+  bookdown::pdf_book:
+    includes:
+      in_header: preamble.tex
+    keep_tex: yes
+    latex_engine: xelatex
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+---
+
+# Prerequisites
+
+This is a _sample_ book written in **Markdown**. You can use anything that Pandoc's Markdown supports, e.g., a math equation $a^2 + b^2 = c^2$.
+
+For now, you have to install the development versions of **bookdown**, **rmarkdown**, and **knitr**:
+
+```{r eval=FALSE}
+install.packages(
+  c("bookdown", "knitr"),
+  repos = c("http://yihui.name/xran", "http://cran.rstudio.com")
+)
+```
+
+Remember each Rmd file contains one and only one chapter.

preamble.tex

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+\usepackage{booktabs}

style.css

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+.kable_wrapper {
+  border-spacing: 20px 0;
+  border-collapse: separate;
+  border: none;
+  margin: auto;
+}
+.kable_wrapper > tbody > tr > td {
+  vertical-align: top;
+}
+p.caption {
+  color: #777;
+  margin-top: 10px;
+}
+p code {
+  white-space: inherit;
+}
+pre {
+  word-break: normal;
+  word-wrap: normal;
+}
+pre code {
+  white-space: inherit;
+}