I wonder if it is possible to put an appendix after references when using biblatex. These question and answer or this answer showed how to do so without citation_package: biblatex but do not work anymore when I add this in YAML. Using child document to print appendix after references does not work either.
Is it possible to use both biblatex and this solution?
Here's a reproducible example (Not working. Remove citation_package: biblatex for a functional example):
---
title:
author:
date:
abstract:
output:
pdf_document:
number_sections: true
citation_package: biblatex
bibliography: references.bib
biblio-style: bwl-FU
---
# Part 1
#greenwood_financial_1989
# My references
<div id="refs"></div>
# Appendix
bla bla
with references.bib:
#article{greenwood_financial_1989,
title = {Financial Development, Growth and the Distribution of Income},
url = {https://www.nber.org/papers/w3189},
number = {3189},
journaltitle = {NBER Working Paper Series},
date = {1989},
author = {Greenwood, Jeremy and Jovanovic, Boyan}
}
Edit: As suggested, I compared the latex document produced by the .Rmd file (by adding keep_tex: true in YAML) when I use citation_package: biblatex and when I don't.
I renamed the section "References" as "My references" in the .Rmd file to be able to distinguish the two sections in the latex document.
It appears that:
using citation_package: biblatex automatically adds \printbibliography at the end of the latex document, hence the "References" section with the actual references at the end of the PDF output. Besides, the section "My references" only contains \hypertarget{refs}{}.
when I remove citation_package: biblatex, the \printbibliography line disappears from the latex document, and the "My references" section contains \leavevmode\hypertarget{}{} with the id of the reference and its full description (that I do not paste here because it would only make this less readable).
Therefore, I guess this problem appears during the conversion from the .Rmd file to .tex format.
Related
I am writing a report with R Markdown in which I include references. The problem is that R markdown automatically places references at the end of the report. I would like to place an Appendix after the references, is there a way to do it? I saw that it is possible with a child document but I would like to have everything in a unique .Rmd file.
Below is a reproducible example:
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
citation_package: biblatex
bibliography: references.bib
biblio-style: bwl-FU
---
# Partie 1
\cite{greenwood_financial_1989}
<!-- where I would like the references to be -->
# Appendix
bla bla
and here is the content of the references.bib file:
#article{greenwood_financial_1989,
title = {Financial Development, Growth and the Distribution of Income},
url = {https://www.nber.org/papers/w3189},
number = {3189},
journaltitle = {NBER Working Paper Series},
date = {1989},
author = {Greenwood, Jeremy and Jovanovic, Boyan}
}
Any idea ?
This is explained in the R Markdown Cookbook (section 3.5.4). We can force the bibliography to be printed at a particular place with:
# References
<div id="refs"></div>
# Appendix
Note that:
this works if we cite the papers with #id_of_paper (which is the recommended way in R Markdown) but not with \cite{id_of_paper}.
this does not work if we use citation_package: biblatex in YAML
Here's my adapted example:
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
bibliography: references.bib
biblio-style: bwl-FU
---
# Partie 1
#greenwood_financial_1989
# References
<div id="refs"></div>
# Appendix
bla bla
If using
citation_package: biblatex
you can include the bibliography at an arbitrary point using
\printbibliography
This does not, of itself, stop pandoc adding a (further) end-of-document bibliography, but since pandoc ignores latex in non-latex output, we can suppress that by redefining \printbibliography on the fly to do nothing.
So try this, for a references section preceding an Appendix:
# References
<div id="refs"></div>
\printbibliography[heading=none]
\def\printbibliography{}
# Appendix 1
Appendix goes here, and is not followed by a bibliography.
I am writing a report with R Markdown in which I include references. The problem is that R markdown automatically includes references at the end of the report (without calling them with \printbibliography for example) and the section title is "References". I am writing in French so I would like the title to be "Références", but more generally is there any way to modify the title of that section?
Below is reproducible example:
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
citation_package: biblatex
bibliography: references.bib
biblio-style: bwl-FU
---
# Partie 1
\cite{greenwood_financial_1989}
# Partie 2
bla bla
and here is the content of the references.bib file:
#article{greenwood_financial_1989,
title = {Financial Development, Growth and the Distribution of Income},
url = {https://www.nber.org/papers/w3189},
number = {3189},
journaltitle = {NBER Working Paper Series},
date = {1989},
author = {Greenwood, Jeremy and Jovanovic, Boyan}
}
Does anybody have a solution?
Here's the solution that combines this answer on doing something similar with bibtex and this one on the TeX required to do it in biblatex, plus #Ralf's comment about adding lang: fr
---
title:
author:
date:
abstract:
output:
pdf_document:
template: NULL
number_sections: true
citation_package: biblatex
bibliography: references.bib
biblio-style: bwl-FU
lang: fr
---
In my document, I used :
header-includes:
- \usepackage[french]{babel}
And your Contents section also changes.
I had a similar problem I wanted to place the bibliography above a supplemental section and placing <div id = "refs"></div> where you want the references successfully repositioned the section. I also had no problem renaming the section by simply changing the # title above that section. This did work for PDF output as well as HTML despite appearing to be an HTML only solution, though I was also using the markdown flavored ([#Smith2019]) references in the body of my document I don't know if using the LaTeX style will affect things.
When citation_package: biblatex is included in the YAML of an .Rmd file, is it possible to specify the citation style? I can't find any information on this in the various R markdown manuals.
This issue was resolved in March 2016. As a lot of the documentation was written before this, it doesn't always show up in the guidance. However, the NEWS file on rmarkdown is always a good place to check for new features.
You can use the biblio-style argument within the YAML. If you are familiar with latex, this is basically filling in the \usepackage[style= *SELECTED STYLE*]{biblatex}. Here is an example. It will build a separate .bib file for you:
---
output:
pdf_document:
citation_package: biblatex
keep_tex: TRUE
bibliography: test.bib
---
```{r}
knitr::write_bib(x = c("knitr", "rmarkdown") , file = "test.bib")
```
Some ref [#R-knitr]
Another ref [#R-rmarkdown]
# References
This outputs:
Adding the biblio-style argument:
---
output:
pdf_document:
citation_package: biblatex
keep_tex: TRUE
bibliography: test.bib
biblio-style: authoryear
---
```{r}
knitr::write_bib(x = c("knitr", "rmarkdown") , file = "test.bib")
```
Some ref [#R-knitr]
Another ref [#R-rmarkdown]
# References
To find out more about different styles you can use, check here: https://www.sharelatex.com/learn/Biblatex_citation_styles
Taking this further: the YAML only provides a certain amount of control of the biblio-style. For example, you cannot specify citestyle directly. if you want to go further with changing the biblatex style, you will need to edit the pandoc template: https://github.com/rstudio/rmarkdown/blob/master/inst/rmd/latex/default-1.15.2.tex . This is a bit more advanced though, so only recommend it if you are comfortable with LaTex: https://rmarkdown.rstudio.com/pdf_document_format.html#custom_templates
Hum, i trying to understand how R Bookdown generate different html output to migrate easily my phd actually in latex on a html website.
\usepackage[backend=biber,backref=true, natbib=true, isbn=false, doi=true, url=true, style=authoryear,maxcitenames=1, maxbibnames=999, sorting=nyt, refsection=chapter, hyperref]{biblatex}
As you can see, my thesis use biblatex with biber and natbib which permit me to use \autocite and \autocites command. I try multiple configuration to reuse this type of citation directly in markdown (and not [#key] or #key citation), without success.
I start with simple things in index.Rmd :
---
title: "A Minimal Book Example"
author: "Yihui Xie"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
bibliography: [these.bib]
biblio-style: apalike
latex_engine: xelatex
citation_package: natbib
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."
---
# Introduction
test my citation with \autocite{Pumain1997}.
these.bib contain this simple citation :
#article{Pumain1997,
author = {Pumain, Denise},
doi = {10.3406/spgeo.1997.1063},
issn = {0046-2497},
journal = {Espace g\'{e}ographique},
number = {2},
pages = {119--134},
title = {{Pour une th\'{e}orie \'{e}volutive des villes}},
url = {http://www.persee.fr/web/revues/home/prescript/article/spgeo\_0046-2497\_1997\_num\_26\_2\_1063},
volume = {26},
year = {1997}
}
You need to keep in mind that following rules are applied when rendering the Rmd file
bookdown specific commands will be translated by bookdown into the relevant LaTeX\HTML equivalent
markdown will be converted by pandoc into the relevant LaTeX\HTML equivalent
LaTeX (HTML) will be passed as is when the output format is LaTeX (HTML)
LaTeX (HTML) will be ignored when the output format is HTML (LaTeX)
Bottom line: use #key and [#key] in case you want to convert the document to both LaTeX and HTML
I'm currently preparing a presentation in RStudio (using RMarkdown and Knitr, outputting to a Beamer presentation) that has quite a few references.
I'm using a pretty typical YAML header:
---
title: "Title"
author: "Me"
date: "February 27th, 2016"
output:
beamer_presentation
csl: ../../apa.csl
bibliography: ../../RefenceDesk.bib
---
This presentation compiles and the references appear as they should, but unfortunately they all appear on one slide (and actually run off the page). Is there any way to have the references appear on multiple slides?
{.allowframebreaks} is the solution for multislides bibliographies in beamer. It works out of the box with regular pandoc templates (see my previous answer). However, knitr has a setting that prevents it, by redefining \widowpenalties in its beamer template. You can verify that if you examine the .tex file with keep_tex: true.
In my opinion, this is a bug. A quick fix would be to reset \widowpenalties to its default value. It can be done in your yaml front matter:
---
title: Title
header-includes:
- \widowpenalties 1 150
output:
beamer_presentation
---
Then, you can indicate the reference section as such:
## References {.allowframebreaks}
As #David above said in the comments:
For me it didnt work with ## References {.allowframebreaks} but it worked out with # References {.allowframebreaks}.
I would like to point out that, apparently for the reference slide to work you have to create a last slide with the same heading level es set by slide_level: __ at the YAML section.
So, the user should set one of the following:
# References {.allowframebreaks}. for those using slide_level: 1, OR
## References {.allowframebreaks}. for those using slide_level: 2, OR
### References {.allowframebreaks}. for those using slide_level: 3 and so on...
While this goes outside of using the regular pandoc citation template, I have found another approach that can be used to put the references across slides but it relies on the natbib citation package.
In the YAML front matter, I added:
---
title: "Title"
output:
beamer_presentation:
citation_package: natbib
bibliography: ../../RefenceDesk.bib
biblio-style: "apalike"
---
The reference slide does not get a title and I cannot seem to adjust the font size (by using a \scriptsize at the end of the .Rmd file), but at least they appear coherently.
EDIT: For parsimony, I removed the csl: ../../apa.csl line, since natbib does not require it.