How to move the bibliography in markdown/pandoc

16
votes

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?

3
rmarkdownknitrpandoc
Very interesting question, would like to do exactly the same! – waeltken
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

3 Answers

17
votes

There is another solution:

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

It lets you put the references wherever you want.

9
votes

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
0
votes

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.