CODEWITHSUNDEEP
rr-markdownbookdown
David L Thiessen
David L Thiessen

Reputation: 694

Why does _output.yml prevent me from moving references in bookdown::pdf_book()?

The top voted answer to this question, How to move the bibliography in markdown/pandoc, says that you can control the location of the references in rmarkdown/pandoc by adding <div id="refs"></div> where the references are supposed to appear. This does not work in the pdf_book format from the bookdown package if _output.yml contains a pdf_book output. An example is a directory containing two files:

_output.yml

bookdown::gitbook:
bookdown::pdf_book:
  latex_engine: xelatex
  citation_package: natbib
  keep_tex: yes

index.Rmd

--- 
title: "An example"
author: "Me"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [packages.bib]
biblio-style: apalike
link-citations: yes
---

# Prerequisites

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

I want references *here*

<div id="refs"></div>

# Introduction

We are using the **bookdown** package [@R-bookdown].

Calling bookdown::render_book(output_format = 'bookdown::pdf_book') creates a pdf file that has references at the end of the document, not at the location specified by <div id="refs"></div>. In contrast calling bookdown::render_book(output_format = 'bookdown::gitbook') does place the references at the specified location.

If I delete _output.yml or delete the pdf_book section,

_output.yml

bookdown::gitbook:

Then running bookdown::render_book(output_format = 'bookdown::pdf_book') does place the references in the correct location.

My package version info is:

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042), RStudio 1.4.1103

Locale:
  LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252   
  LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
  LC_TIME=English_Canada.1252    

Package version:
  assertthat_0.2.1  base64enc_0.1.3   bookdown_0.21.6   callr_3.5.1      
  cli_2.3.0         compiler_4.0.3    crayon_1.4.1      curl_4.3         
  desc_1.2.0        digest_0.6.27     evaluate_0.14     glue_1.4.2       
  graphics_4.0.3    grDevices_4.0.3   highr_0.8         htmltools_0.5.1.1
  jsonlite_1.7.2    knitr_1.31        magrittr_2.0.1    markdown_1.1     
  methods_4.0.3     mime_0.10         pkgbuild_1.2.0    prettyunits_1.1.1
  processx_3.4.5    ps_1.5.0          R6_2.5.0          remotes_2.2.0    
  rlang_0.4.10      rmarkdown_2.7.1   rprojroot_2.0.2   rstudioapi_0.13  
  stats_4.0.3       stringi_1.5.3     stringr_1.4.0     tinytex_0.29     
  tools_4.0.3       utils_4.0.3       withr_2.4.1       xfun_0.21        
  yaml_2.2.1

Why does having an otherwise valid _output.yml prevent me from changing the location of the references? Are there options I can add to _output.yml that will make pdf_book respect <div id="refs"></div>?

Upvotes: 0

Views: 326

Answers (1)

cderv
cderv

Reputation: 6542

From the answer I posted on Github https://github.com/rstudio/bookdown/issues/1082#issuecomment-811026589

Changing placement of the bibliography using a div of id refs as explained in https://bookdown.org/yihui/rmarkdown-cookbook/bibliography.html#include-appendix-after-bibliography is a Pandoc citation processor feature. See https://pandoc.org/MANUAL.html#placement-of-the-bibliography

Using Pandoc's citeproc is the default for pdf_document() and pdf_book(), but here n your output file _output.yml, you are explicitly changing citation_package to natbib for the bookdown::pdf_book format.

When you call bookdown::render_book(output_format = 'bookdown::pdf_book'), depending on the case you tested, this will happen

  • if the format is defined in _output.yaml it will use the configuration define there and use natbib
  • if the format is not defined in _output.yaml it will use the default config for the format and --citeproc will be use.

You can only control the placement of the bibliography with a div of id refs in the second case.

You just need to change the citation_package: accordingly to want you need, and remove the field if you want to use Citations features from Pandoc processor.

Upvotes: 2

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