How to move the bibliography in markdown/pandoc

Question

I'm currently writing my bachelor thesis and my instructor wants me to put my appendix after the bibliography but markdown/pandoc puts the references at the end by default. I read the instructions at http://yihui.name/knitr/demo/pandoc/ and tried to use the include-after-body=FILE command to put a separate .rmd file at the end of the document My code looks like this:

```{r, echo=FALSE, warning=FALSE, message=FALSE}
library(knitr)
pandoc('thesis.rmd', format="latex")
```

and for the options:

<!--pandoc
t: latex
include-after-body: appendix.rmd
o: output.pdf
-->

Where appendix.rmd is the separate appendix file.

After klicking on convert pdf, the process gets stuck with an error after the line executing pandoc --include-after-body=appendix.rmd -o thesis.pdf -f markdown -t latex -o thesis.pdf "thesis.utf8md"

The error is:

pandoc.exe: Error producing PDF from TeX source.

Is there something wrong with the code or is there some other method to remove the bibliography from the end of the document?

Very interesting question, would like to do exactly the same! — waeltken, Aug 21 '15 at 17:20
Well it's been a while since I had the problem so maybe there is another solution but I used a workaround which is a bit messy but it did the job. I first created a pdf without the appendix and the bibliography at the end and afterwards created another pdf which only contained the appendix, without page numbers and put the two pdf documents together. I know it's not ideal but my thesis advisor was fine with it, so maybe it helps you as well. — mockstr, Aug 22 '15 at 18:57

Thomas Reiss · Answer 1 · 2018-05-04T08:17:05.490

20

There is another solution:

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

It lets you put the references wherever you want.

edited May 04 '18 at 08:17

answered Jun 14 '17 at 13:59

Thomas Reiss

267
3
10

For me, this did the trick! Thank you! Note: it also works for docx. – January Mar 28 '19 at 13:22
I don't think this trick works with LaTeX output, as the OP seemed to want. – Maurizio Tomasi Apr 11 '19 at 14:36
It also works for LaTeX, but not properly in combination with biblatex. – der_grund Aug 28 '19 at 12:05

Andrew · Answer 2 · 2020-11-20T18:36:48.123

17

You can place your bibliography wherever you like by inserting

::: {#refs}
:::

wherever you want the bibliography printed. From the "Placement of the bibliography" section of the pandoc markdown manual.

For example:

...main body

# References

::: {#refs}
:::

# Appendix

edited Nov 20 '20 at 18:36

answered Oct 03 '19 at 20:55

Andrew

490
3
9

2

https://pandoc.org/MANUAL.html#placement-of-the-bibliography is probably a more accurate link to the documentation for what you are discussing. – Clément Nov 19 '20 at 05:42
Apparently this only works for certain styles ("If the style calls for a list of works cited, it will be placed in a div with id `refs`, if one exists"). For instance, the [eisvogel](https://github.com/Wandmalfarbe/pandoc-latex-template) template does not support this. – Christoph Thiede Feb 11 '23 at 13:11

score 0 · Answer 3 · answered Dec 21 '16 at 10:09

I just figured out that it works when you use a tex file, like --include-after-body=appendix.tex. I'm not an RMarkdown or Tex expert at all but I could imagine that it will only include the file after your main Rmd is already converted to a tex file using the default template.

How to move the bibliography in markdown/pandoc

3 Answers3

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