Reference list at bottom of each html page has disappeared...

[BackseatPete]

Hi all

I've been using bookdown for a while now... but lately I have noticed that the reference list that used to appear at the bottom of each webpage is no longer there.

For example, when I look at one of the chapters in the bookdown manual, there is a reference list at the bottom of the pages when relevant. So it must still be the way it works; nothing has changed.

But this is not so for any of my bookdown documents (including when I compile the default template "Book Project using bookdown" document in RStudio, so it must not be anything in my documents).

In addition, my last-chapter Reference list looks far more squashed and very hard to read compared to other bookdown books.

All the references appear OK, and the links work OK. But there must be an issue somewhere. Since it doesn't appear elsewhere, and the the issues appear with the template document too, perhaps it is an issue with my system somehow.

But I have no idea where to start looking. Any idea where to start looking, or how to fix?

Thanks.

P.

PS: Also posted on stack overflow about two weeks ago, but no reply

[cderv]

Can you share the Pandoc version your are using ?

rmarkdown::find_pandoc()

I assume this it is greater than 2.11.

We fixed a bunch of issues recently, specifically some related to references because Pandoc has changed some processing for citation.

Can you try with dev bookdown ?

remotes::install_github('rstudio/bookdown')

Thank you !

[BackseatPete]

Thanks for the reply.

rmarkdown::find_pandoc()
$version
[1] ‘2.11.2’

I updated with dev bookdown.

This fixed one of the issues, so thanks: Now the references appear at the bottom of each html page. Thanks heaps.

However, the lists of References on each html page, as well as the last-chapter list of References, still look awful and squashed (which is not what used to happen). And this happens whether I use biblio-style: plain in my index.Rmd file, or if I comment out this line.

(See attached image (or links (updated) in original post) , which has five references but it is very hard to delineate them.)

So thanks for the fix. Any idea on the formatting of the Reference lists?

P.

[cderv]

Bibliography style can depend on the style you asked for. If you use the default, and you use Pandoc citeproc it is possible that the defaut as changed.

You can use a CSL if you want to customize:

4.5 Bibliographies and citations | R Markdown Cookbook

See the reference page in the cookbook, it looks the same : References | R Markdown Cookbook

So I am not sure if there is an issue - or just you need to choose a style that suits you

[BackseatPete]

Thanks again.
But I think you missed my point (because I failed to explained it well enough).

The actual style doesn't bother me greatly at all.

But the annoying thing is, whatever reference style I specify, the references are always in a really-squashed up, hard-to-read format.

For example, two images are attached.

• One is using csl: csl: journal-of-applied-animal-science.csl (journal titles not in bold).
• The other using csl: academy-of-management-review.csl (journal titles in bold).

The style changes (as one would expect, so I am doing the right thing I think)... but in both cases, the references are so squashed it hard to see the individual entries.

This never used to be the case; there used to be a small vertical space between the individual entries.

Any thoughts? Thanks for your time.

P.

[cderv]

Thanks for the explanation. I see what you mean now.

Is it with the default gitbook format ?

This is a styling issue / preference. I don't really now what is the difference from Pandoc. You are using 2.11.2 and 2.13 is out now. They may have tweak this CSS style for CSL reference maybe.

I believe you can do it with adding a small css like

.csl-entry {
    padding-bottom: 1em;
}

Before:

After:

We should check with default Pandoc template what style we get and maybe update gitbook's template in bookdown if we missed some CSS.

Thanks for sharing this.

[BackseatPete]

Thanks so much cderv!

That works a treat.

I know that the entries in the reference list did used to be separated like that... then it changed. No idea why.

Thanks.

P.

[cderv]

I have check and it leads to the same with last Pandoc (without R Markdown involved).
I assumed the update to Pandoc 2.11 and new citeproc have changed the default style.

I don't think this is an issue on our side.

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