Pandoc Insert Appendix After Bibliography

Pandoc insert appendix after bibliography

Eventually reference handling will change to make it possible to put the references wherever you like (https://github.com/jgm/pandoc/issues/771), but right now there's no easy way to do it.

As suggested here, you could put your appendix in a separate file, use pandoc to convert it to a LaTeX fragment, then include that fragment using the --include-after-body flag. It would then come after the bibliography.

R Markdown: place an Appendix after the References section?

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 

Adding figures and tables after bibliography in Rmarkdown

Rather than trying to include things in the after_body, you are better off just repositioning where the bibliography appears in the document. As explained in this answer, you can choose where the bibliography appears using <div id="refs"></div>.

Secondly, you can use bookdown to easily add appendices within a document. Using the header # (APPENDIX) Appendix {-} will change all following secton numbers from numbers to letters. Check out the bookdown book

Used in a full example:

---
title: "Untitled"
output: bookdown::pdf_document2
references:
- id: fenner2012a
  title: One-click science marketing
  author:
  - family: Fenner
    given: Martin
  container-title: Nature Materials
  volume: 11
  URL: 'http://dx.doi.org/10.1038/nmat3283'
  DOI: 10.1038/nmat3283
  issue: 4
  publisher: Nature Publishing Group
  page: 261-263
  type: article-journal
  issued:
    year: 2012
    month: 3
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(magrittr)
```

# Introduction

Here is a citation [@fenner2012a]

# References {-}

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

\newpage 

# (APPENDIX) Appendix {-}

# Appendix A

Here is your table

```{r table, fig.pos="H"}
knitr::kable(mtcars[1:5, 1:5], caption = "A table") %>%
  kableExtra::kable_styling(latex_options = "HOLD_position")
```

Note: this will only work if you use pandoc's built-in citation package and won't work if you set citation_package: natbib in the YAML

Include Rmd appendix after references

In order to have appendices after the references, you simply include a div with id="refs" which tells pandoc where to include the references section. For example:

```{r, child = "08_discussion.Rmd"}
```

# References

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

```{r, child = "09_appendix.Rmd"}
```

Credit: https://twitter.com/tjmahr/status/763435602935095296

Pandoc: Is there a way to include an appendix of links in a PDF from markdown?

This is something that is easy to achieve with filters.

Here is linkTable.hs. A filter which adds a table of links to the end of your document.

import Text.Pandoc.JSON
import Text.Pandoc.Walk
import Data.Monoid

main :: IO ()
main = toJSONFilter appendLinkTable

appendLinkTable :: Pandoc -> Pandoc
appendLinkTable (Pandoc m bs) = Pandoc m (bs ++ linkTable bs)

linkTable :: [Block] -> [Block]
linkTable p = [Header 2 ("linkTable", [], []) [Str "Links"] , Para links]
  where
    links = concatMap makeRow $ query getLink p
    getLink (Link txt (url, _)) = [(url,txt)]
    getLink _ = []
    makeRow (url, txt) = txt ++ [Str ":", Space, Link [Str url] (url, ""), LineBreak]

Compile the filter with ghc linkTable.hs. The output is as follows.

> ghc linkTable.hs 
[1 of 1] Compiling Main             ( linkTable.hs, linkTable.o )
Linking linkTable ...

> cat example.md 
Title
-----

[Python][] is cool!

[Pip] is a package manager.

...

[Python]: http://python.org
[Pip]: https://pip.readthedocs.org

Then running pandoc with the filter.

> pandoc -t markdown --filter=./linkTable example.md
Title
-----

[Python](http://python.org) is cool!

[Pip](https://pip.readthedocs.org) is a package manager.

...

Links {#linkTable}
-----

Python: <http://python.org>\
Pip: <https://pip.readthedocs.org>\

---

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