How to Insert Appendix After References in Rmd Using Rstudio

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

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

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.

Including citation and references when using appendix on RMarkdown

So, I did actually find a solution that does use some minor trickery.

---
bibliography: bb.bib
fontsize: 11pt
nocite: '@*'
output:
  pdf_document:
      keep_tex: true
      includes:
        after_body: Demo2.tex
link-citations: true
---

```{r,include=FALSE}
library(tidyverse)
rmarkdown::render('Demo2.Rmd')
a <- readChar('Demo2.tex', file.size('Demo2.tex'))
a <- a %>% str_remove('[[:space:]]*\\\\hypertarget[[\\w\\W]]+\\z') %>%
  str_remove('\\A[[\\w\\W]]+begin.document.')
writeChar(a, 'Demo2.tex',eos = NULL)
```

\newpage

\section{Testing}\label{sec1}
```{r}
summary(cars)
```

\section{Demo}
This was done using @shiina and we will use some info from Section \ref{sec1} to do.
```{r}
summary(iris[,1:2])
```
\section{References} 

---

And your Appendix-file:

---
bibliography: bb.bib
fontsize: 11pt
output:
  pdf_document:
      keep_tex: yes
link-citations: true
---

\appendix
\section*{Appendix}
\section{Additional info}
In this section we also follow @shiina to explain concepts.

# References

---

results in:

---

The way it works is to render the Demo2.Rmd- file before rendering the actual file and to keep the associated .tex- file.
Then the non included R-chunk cuts of all the parts we don't want to have at the end of the main file and overwrites the Demo2.tex-file.
What remains is the exact tex-code you need to have your references working.

Feels pretty dirty, but should work.

Placing literature references in a table in Rmd

ftExtra may be solution here:

---
title: "test"
author: "David"
date: "27/01/2021"
output: html_document
bibliography: test.bib
---

test[@guan_clinical_2020]

``` {r, echo = F}
library("flextable")
library("ftExtra")
dat <- dplyr::tibble("study_id" = c(1,2),
               "lead_author" = c("Guan, Ni", "Guan, Liang"),
               "sample_size" = c(1099, 1590),
               "refs" = c("[@guan_clinical_2020]",
                          "[@guan_comorbidity_2020]"))
dat %>%
  flextable() %>%
  colformat_md() %>%
  autofit()
```

---

Related Topics