How to accumulate `packages.bib` used in a Quarto book

R Markdown
#1

[This question was posed in a Quarto discussion, but they deemed it not a Quarto problem. I'm hoping to get some help here.]

I'm writing a book with multiple chapters and wish to generate a packages.bib file at
the end containing citations for all the packages that were loaded via library()
while the book is compiled by "Render book". I know how to do this for a vignette, but not
for a multi-chapter quarto book.

In vignettes I use the following to automatically generate a packages.bib file for all
the packages used, so that I can easily cite them as needed:

  • In the preamble I list a few packages which may be referred to in the text, but not
    actually loaded by library() 
# packages to be cited here. Code at the end automatically updates packages.bib
.to.cite <- c("nnet",  "geomtextpath")
  • Then, at the end, just before ## References I use this chunk to join .to.cite with
    .packages() and write this out using knitr::write_bib():
```{r write-bib, echo = FALSE}
# write a packages.bib file of the packages (.packages()) that have been used here
pkgs <- unique(c(.to.cite, .packages()))
knitr::write_bib(pkgs, file = here::here("vignettes", "packages.bib"))
```
#2

Maybe you can do a similar process but differently. Quarto books differs by the fact R will be run for each file separatly. So you can't store your package list in a R value in the session. You need to store it on disk or any persistent storage.

Now at the end of each .qmd, you could add a chunk that would store the loaded package, and other packages in a file on disk, and at the end produce the bib file. Maybe you could produce the bib file each time, and append to it too (There are packages to read and write bib file like CRAN - Package rbibutils or CRAN - Package bibtex) .

Though the order of execution matters. By "at the end" it could be

  • Updating the bibfile after each document
  • Producing the bibfile at the last .qmd processed
  • Using post render script in Quarto project maybe Quarto - Project Scripts

Just ideas that I am brainstorming. There is no built in way to do that in Quarto so you need to come up with your own R workflow for this.

Please keep us updated on this !

#3

That is very helpful. I didn't know how Quarto processed chapters in a book, and was still thinking in the knitr/Rmarkdown mode.

A related question: What controls whether Quarto generates References for each chapter or at the end? Is it possible to do both?

#4

Not sure to understand. Where do you want the references ?

There are some options like reference-location or citation-location possible (see in the doc website), but not sure that is what you want.

Pandoc citeproc is doing a lot of the citation processing too.

#5

Hi @cderv
I found a solution to this by appending names of packages used in each chapter to a file, then reading that in in the last chapter.

Here is a Github gist describing what I did.

Perhaps someone else will find this useful.

1 Like
#6

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.

#7

Looks like a good solution ! Thank you for sharing!