Bibliography with knitr : cite your references and packages

February 2, 2019
By

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A tutorial to use your Zotero references with rmarkdown, easily add the references, automatically generate your bibliography, including the packages used in your document.

It’s a good practice to cite the R packages you use in your analysis. However it can be cumbersome to maintain the list of your package’s references in Zotero while the packages used can change in your script. Here we use the automatic updates of Zotero to generate our main bibliography and we auto-generate the package bibliography and then merge them.

Prerequisites

Install R, Rstudio, Zotero.

Install Better BibTex for Zotero.

To easily add citations in the rmarkdown text in RStudio, we can add the citr package.

Build the Zotero library

Add references to Zotero.

Create a collection for our project.

Zotero

Export the collection (BibLatex format). Tick the update option.

Export

We save it in our R project folder as zotero.bib. Each time we modify our Zotero collection, the zotero.bib file will be updated. Check in the Zotero settings :

Preferences

We can also add a personalized CSL file (used to format references) in your R project folder (see the repository). Below I chose ISO-690 (author-date, no abstract, French).

In our rmarkdown text

In the setup chunk, we load the required packages, generate the .bib file for the packages, merge it with our Zotero bibliography and add the packages as nocite (they are not cited in the text but have to appear in the references).

We must run the setup chunk at least once to generate the files and check which citation to use for the packages that provide multiple references.

We can then carry on our analysis with R chunks and some text with citations.

The citations can be added with [@key] where key is the citation key generated by Better Bibtex and found at the top of the Zotero info panel. Or we can use citr which will help us find it.

---
title: "Bibliography with knitr : cite your references and packages"
author: "r.iresmi.net"
date: "`r Sys.Date()`"
output: html_document
bibliography: biblio.bib
csl: iso690-author-date-fr-no-abstract.csl
link-citations: yes
---

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

# all your necessary packages
packages <- c("tidyverse", 
             "knitr",     
             "bibtex"
             # add your other packages here     
             )  

# install if needed and loading packages
to_install <- packages[! packages %in% installed.packages()[, "Package"]]
if (length(to_install)) { 
  install.packages(to_install, repos = "https://cloud.r-project.org")
}
invisible(lapply(packages, library, character.only = TRUE))

# get the packages version 
packages_versions <- function(p) {
  paste(packageDescription(p)$Package, packageDescription(p)$Version, sep = " ")
}

# Get the packages references
write.bib(packages, "packages.bib")

# merge the zotero references and the packages references
cat(paste("% Automatically generated", Sys.time()), "\n% DO NOT EDIT",
    { readLines("zotero.bib") %>% 
      paste(collapse = "\n") },
    { readLines("packages.bib") %>% 
      paste(collapse = "\n") },
    file = "biblio.bib",
    sep = "\n")


# Some packages reference keys must be modified
# (their key is not the package name)
# check in packages.bib
packages_keys <- packages %>% 
  enframe() %>% 
  mutate(value = case_when(value == "knitr" ~ "@knitr1",
                           #value == "boot" ~ "@boot1",
                           TRUE ~ paste0("@", value)))
```

---
nocite: |
  @Svenssonguideornitho2007
  `r paste(packages_keys$value, collapse = "\n  ")`
---

Any text...

Data analyzed with R [@r_development_core_team_r:_2010][^r_version].

[^r_version]: `r version$version.string`, with : `r paste(lapply(sort(packages), packages_versions), collapse = ", ")`.

We can easily cite references (menu Addins / Insert citations) after having run the setup chunk to create the bibliography file [@moreno_measuring_2017].

Lorem Ipsum

## References

After knitting we get the file :

knitted

See the result.

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