How to Add Chapter Bibliographies Using Bookdown

Is there a way to add chapter bibliographies using bookdown?

For HTML output the default is to use per-chapter bibliographies. For PDF output, I have found it is best to use the LaTeX package biblatex together with biber. Since RStudio does not know about biber, it is best to install a tool like latexmk and configure RStudio to use that via Sys.setenv(RSTUDIO_PDFLATEX = "latexmk"). These programs might have to be installed separately, e.g. on Debian/Ubuntu/...

sudo apt-get install texlive-bibtex-extra biber latexmk

For configuring biblatex the solution provided at https://tex.stackexchange.com/questions/199336/biblatex-reference-both-by-chapter-and-at-the-end-of-the-book is appropriate.

In the end the following settings are necessary in _output.yml:

bookdown::pdf_book:
  citation_package: biblatex

In Index.Rmd:

biblio-style: authoryear
biblatexoptions: [refsegment=chapter]

At the end of every chapter:

\printbibliography[segment=\therefsegment,heading=subbibliography]

There is no need to escape this raw LaTeX command, since pandoc ignores such commands for other output formats.

One can see the entire solution at

https://github.com/rstub/bookdown-chapterbib
https://rstub.github.io/bookdown-chapterbib/
https://rstub.github.io/bookdown-chapterbib/bookdown-chapterbib.pdf

Original solution

I managed to get chapter bibliographies with PDF output using the following steps:

Start with a copy of https://github.com/rstudio/bookdown-demo
copy <R-library-path>/rmarkdown/rmd/latex/default-1.17.0.2.tex as book.tex to the working directory
update book.tex to use the LaTeX package bibunits (diff below)
update _output.yml to refer to book.tex as template (diff below)
set YAML options in index.Rmd (diff below)
add code to some Rmd files to write \putbib command (diff below)

After these changes, a PDF file could be produced, but all references where missing, since bookdown does not know about the generated bu?.aux files. After executing bibtex bu1 and bibtex bu2, reproducing the PDF file via bookdown produced a PDF with chapter bibliographies. It is probably best to automate this step with Makefile.

Here the diff between the templates:

$ diff -u /usr/local/lib/R/site-library/rmarkdown/rmd/latex/default-1.17.0.2.tex  book.tex
--- /usr/local/lib/R/site-library/rmarkdown/rmd/latex/default-1.17.0.2.tex  2017-12-11 19:14:54.643867696 +0100
+++ book.tex    2018-01-16 11:43:46.182542634 +0100
@@ -93,8 +93,11 @@
 \fi
 $endif$
 $if(natbib)$
-\usepackage{natbib}
+\usepackage[$natbiboptions$]{natbib}
 \bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+\usepackage{bibunits}
+\defaultbibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+\defaultbibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
 $endif$
 $if(biblatex)$
 \usepackage$if(biblio-style)$[style=$biblio-style$]$endif${biblatex}
@@ -235,6 +238,7 @@
 $endfor$

 \begin{document}
+\bibliographyunit[\chapter]
 $if(title)$
 \maketitle
 $endif$

And the diff of the files from bookdown-sample:

$ git diff
diff --git a/01-intro.Rmd b/01-intro.Rmd
index 6b16e73..1a5f9de 100644
--- a/01-intro.Rmd
+++ b/01-intro.Rmd
@@ -19,3 +19,5 @@ knitr::kable(
 ```

 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].
+
+`r if (knitr:::is_latex_output()) '\\putbib'`
diff --git a/02-literature.Rmd b/02-literature.Rmd
index 00745d0..983696e 100644
--- a/02-literature.Rmd
+++ b/02-literature.Rmd
@@ -1,3 +1,6 @@
 # Literature

 Here is a review of existing methods.
+[@R-knitr]
+
+`r if (knitr:::is_latex_output()) '\\putbib'`
diff --git a/_output.yml b/_output.yml
index 342a1d6..cc8afb1 100644
--- a/_output.yml
+++ b/_output.yml
@@ -14,4 +14,5 @@ bookdown::pdf_book:
   latex_engine: xelatex
   citation_package: natbib
   keep_tex: yes
+  template: book.tex
 bookdown::epub_book: default
diff --git a/index.Rmd b/index.Rmd
index 4e21b9d..2fdb813 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -7,6 +7,8 @@ output: bookdown::gitbook
 documentclass: book
 bibliography: [book.bib, packages.bib]
 biblio-style: apalike
+natbiboptions: sectionbib
+graphics: yes
 link-citations: yes
 github-repo: rstudio/bookdown-demo
 description: "This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook."

Include after_body in toc with bookdown

I managed to do this by changing the \textbf to \chapter, and include this in the preamble.tex:

\usepackage{fancyhdr}
\pagestyle{fancy}
\setlength{\headheight}{13.6pt} % as requested by fancyhdr's warning

\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
\makeatletter
\renewcommand{\chaptermark}[1]{%
  \if@mainmatter
    \markboth{Chapter \thechapter{}: #1}{}%
  \else
    \markboth{#1}{}%
  \fi
}

As taken from this post

How to put citations (using BibTex) at the last chapter only (instead of at the end of every chapters)?

I assume you areusing the default bookdown::gitbook for HTML output. In that case you can adjust the split_bib variable via YAML headers, typically in _output.yml:

bookdown::gitbook:
  split_bib: no

See ?bookdown::gitbook for more options.

Gitbook chapter bibliography not in alphabetical order

$(function(){    var elems = $('#refs').children('div').remove();    elems.sort(function (a, b) {        return b.id > a.id ? -1 : 1;    });    $('#refs').append(elems);});

<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script><div id="refs" class="references">  <div id="ref-Goloboff2016">    <p>Goloboff, P. A., and S. A. Catalano. 2016: TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32:221–238.</p>  </div>  <div id="ref-Goloboff1999">    <p>Goloboff, P. 1999: Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15:415–428.</p>  </div>  <div id="ref-Nixon1999">    <p>Nixon, K. C. 1999: The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15:407–414.</p>  </div>  <div id="ref-Goloboff1997">    <p>Goloboff, P. A. 1997: Self-weighted optimization: tree searches and character state reconstructions under implied transformation costs. Cladistics 13:225–245.</p>  </div></div>