Referencing from entire zotero library, rather then exported library-user problem

[GabriellaS-K]

Hi,

I am a beginner with R/Rmarkdown, and have just downloaded the better-bibtex to use to reference from zotero, in Rmarkdown. I followed the really helpful setup instructions. However, each time I open R Markdown, and click 'addin', insert citation, a pop up appears (see attached picture)

Then if I connect and load zotero libraries, the references are from my entire zotero, rather than the exported bibliography I saved to the same directory as my markdown file.

YAML header looks like:

  pdf_document: default
  html_document: default
  bibliography: paper_2020.bib

I must be doing something wrong! Sorry for such a basic question, would be grateful for any help!

I originally asked this at the backend and was told this was an issue with the front end :)
Thanks

[crsh]

Hmm, indeed, I think this may be related to citr. If I understand correctly, you want to load the references in paper_2020.bib rather than in Zotero, right?

It seems the addin does not correctly identify the bibliography file in the YAML front matter. Could you try installing citr from this GitHub repository (remotes::install_github("crsh/citr")) to see if that helps? If it doesn't could you provide the R Markdown and Bib-file?

[GabriellaS-K]

Hi,

Thanks for getting back to me. I don't actually mind where the references go, I just thought it was standard practice to have a bibliography file in the same folder as the rmd. I installed citr as you suggested, still no good, it comes up with an error message: Error: bib_file is not a character vector

I can load the zotero connection and synch library like that, but then it doesn't reference correctly. This is the first paper I'm writing in markdown so I'd like to get it right from the start.

below is the copy of the rmd, I"m not sure how to add the bib-file? It says it isn't supported.

Thanks so much for your help!

---
title: "testing reference"
author: "Gabriella"
date: "08/07/2020"
output: html_document
  pdf_document: default
  html_document: default
title : "Referencing
  citation_package: citr
  bibliography: bibliography_HEB.bib

---

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

```{r packages, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
#Installing the referencing package

remotes::install_github("crsh/citr")
```

Just typing to try and reference. Lets try reference Wu et al 2013 `

[crsh]

Sorry for the late response. If you are still interested in debugging this, could you try and remove the white space prior to the bibliography field in the YAML front matter:

bibliography: bibliography_HEB.bib

rather than

  bibliography: bibliography_HEB.bib

Also, remove this line:

citation_package: citr

citr only handles the insertion of the citation keys (e.g., [@author_year]) into the R Markdown document. citation_package controls, which software is used to render the citations when you knit the document (e.g., BibLaTeX or pandoc-citeproc). Unless you have a "nonstandard" usecase, you should be fine just relying on the default.

[manonironside]

Hello, I have been having the same problem as GabriellaS-K when trying to use the RStudio citr Addin: it says bibliography files not found, and shows a blank space after "Bibliography files found in the YAML header". The odd thing is that it sometimes does work, and sometimes doesn't (sometimes within a single R session) and I have no idea why this might be happening. A few extra notes:

• the citr package installed is completely up to date
• No blank spaces in the YAML header, here's my code: bibliography : ["biblio.bib"]
• No problems with creating the bibliography section while knitting. Citations that had already been referenced using the Addin do appear in the knitted references section.

When I re-start an R session, the first time I try to cite, I get the message above that GabriellaS-K posted. The next time I try to do it, I get an error message in the R console:

Error: bib_file is not a character vector

Any clues as to what could be going wrong, or how to fix this?

[Gabriel-Appiah]

I was having the same issue with my Rmarkdown. Error: bib_file is not a character vector. By removing the white space as commented above and restarting RStudio I was able to get citr package to work.