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Open Source Science

https://github.com/crsh/citr

RStudio Addin to Insert Markdown Citations from a BibTeX file or Zotero

https://github.com/crsh/citr

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 9 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

bib bibliographies insert-markdown-citations rstudio-addin

Keywords from Contributors

ropensci tidy-data pandoc geo setup literate-programming rmarkdown book latex visualisation
Last synced: 6 months ago · JSON representation

Repository

RStudio Addin to Insert Markdown Citations from a BibTeX file or Zotero

Basic Info
  • Host: GitHub
  • Owner: crsh
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 3.9 MB
Statistics
  • Stars: 410
  • Watchers: 8
  • Forks: 48
  • Open Issues: 31
  • Releases: 4
Topics
bib bibliographies insert-markdown-citations rstudio-addin
Created over 9 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License

README.Rmd 

---
title   : "citr: RStudio Addin to Insert Markdown Citations"
output  : github_document
---

[![CRAN status](http://www.r-pkg.org/badges/version/citr)](https://cran.r-project.org/package=citr) [![Download counter](http://cranlogs.r-pkg.org/badges/citr)](https://cran.r-project.org/package=citr)
[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![Build status](https://api.travis-ci.org/crsh/citr.svg?branch=master)](https://travis-ci.org/crsh/citr)

`citr` provides functions and an [RStudio addin](https://rstudio.github.io/rstudioaddins/) to search a BibTeX-file to create and insert formatted Markdown citations into the current document.

## Installation

You can either use the stable version of `citr` from CRAN,

~~~r
install.packages("citr")
~~~

or the current development snapshot from this GitHub repository:

~~~r
devtools::install_github("crsh/citr")
~~~


## How to use citr

### The RStudio addin

Once `citr` is installed and you have restarted your R session,  the addin appears in the menus.
Alternatively, you can define a [keyboard shortcut](https://rstudio.github.io/rstudioaddins/#keyboard-shorcuts) to call the addin.

![](tools/images/addin_demo.gif)

The addin will automatically look up the bibliography files specified in the YAML front matter.
If the document does not contain a YAML front matter the addin will attempt to locate a parent document and look up the bibliography file specified therein.
That is, the addin works its automagic even if you edit R Markdown documents that are included as [children](http://yihui.name/knitr/demo/child/) in another R Markdown document.
The expected names of a parent document default to `c("index.Rmd", "master.Rmd")`, it thus works with [`bookdown`](https://bookdown.org/) out of the box, but can be customized (e.g., `options(citr.parent_documents = "my_parent.Rmd")`).


### Using citr without RStudio

The following call searches a bibliography file and creates formatted Markdown citations for the results.

~~~r
library("citr")
md_cite("foo 2016", bib_file = "references.bib")
~~~

`md_cite()` searches the author, year, title, and journal fields of your references.


### Better BibTeX integration
If you are using Zotero `citr` can access your reference database directly.
For this to work, you need to install the [Better BibTeX extension](https://github.com/retorquere/zotero-better-bibtex/wiki).
Once the extension is installed and your reference manager is running, `citr` can access all your references and keep your bibliography file updated by adding missing references.

![](tools/images/addin_zotero_demo.gif)


### Tidying bibliography files
When you are done writing, your bibliography file is likely to contain some unneeded references, which you added while writing but removed during revisions.
`tidy_bib_file()` removes unneeded (or duplicate) entries from your bibliography file.

~~~r
tidy_bib_file(
  rmd_file = "report.Rmd"
  , messy_bibliography = "references.bib"
  , file = "tidy_references.bib"
)
~~~

## Known problems
`citr` relies on `RefManager::ReadBib()` and, thus, indirectly on `bibtex::read.bib()` to load bibliographies.
I have noticed that very long Bib(La)TeX fields can cause these underlying functions to fail (e.g., `Error in do_read_bib(file, encoding = .Encoding, srcfile): lex fatal error: input buffer overflow, can't enlarge buffer because scanner uses REJECT`).
To avoid such problems, I strongly recommend to disable the export of potentially long metadata fields, such as abstract and notes.
The Better BibTeX-plugin allows users to specify fields to omit:

![](tools/images/bbt_omit_abstract.png)

Once, the above error has occurred, it may be necessary to restart the R session.
Otherwise reading any other file may fail with `Error: lex fatal error: fatal flex scanner internal error--end of buffer missed`.


## Other RStudio addins

If you are interested in other handy addins take a look at this [list](https://github.com/daattali/addinslist#readme). There you can find other useful addins, such as [rcrossref](https://github.com/ropensci/rcrossref) or [wordcountaddin](https://github.com/benmarwick/wordcountaddin).

# Package dependencies

```{r dependency_plot, echo = FALSE, fig.width = 7, fig.height = 5, message = FALSE, warning = FALSE, fig.path = "tools/images/"}
source("https://gist.githubusercontent.com/crsh/c906e93c260488e7363ea606243057c2/raw/f6f0fce38bc274446d205854ea35cfa03b9b1f7a/plot_dependencies.R")

plot_dependencies()
```

Owner

  • Name: Frederik Aust
  • Login: crsh
  • Kind: user
  • Location: Cologne, Germany
  • Company: Psychological Methods, University of Amsterdam

GitHub Events

Total
  • Watch event: 6
  • Fork event: 2
Last Year
  • Watch event: 6
  • Fork event: 2

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 107
  • Total Committers: 9
  • Avg Commits per committer: 11.889
  • Development Distribution Score (DDS): 0.159
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Frederik Aust f****t@u****e 90
Ilse Pit i****t@g****m 6
Vilmantas Gegzna G****V@g****m 3
Robin Lovelace r****x@g****m 3
Yihui Xie x****e@y****e 1
TobiasHeycke t****e@u****e 1
Miles McBain m****n@g****m 1
Mara Averick m****k@g****m 1
Garrick Aden-Buie g****e@m****u 1
Committer Domains (Top 20 + Academic)
uni-koeln.de: 2 mail.usf.edu: 1 yihui.name: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 85
  • Total pull requests: 11
  • Average time to close issues: 3 months
  • Average time to close pull requests: 13 days
  • Total issue authors: 61
  • Total pull request authors: 8
  • Average comments per issue: 4.66
  • Average comments per pull request: 2.0
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • crsh (10)
  • Robinlovelace (5)
  • koliajaykr (3)
  • jooyoungseo (3)
  • andreifoldes (2)
  • awmercer (2)
  • nevrome (2)
  • bwiernik (2)
  • heinonmatti (2)
  • ogsteele (1)
  • julou (1)
  • profandyfield (1)
  • llrs (1)
  • statzhero (1)
  • sebacea (1)
Pull Request Authors
  • ilsePit (4)
  • MilesMcBain (1)
  • batpigandme (1)
  • yihui (1)
  • gadenbuie (1)
  • Robinlovelace (1)
  • TobiasHeycke (1)
  • GegznaV (1)
Top Labels
Issue Labels
bug (18) enhancement (17) more-information-needed (5) question (4) upstream (3) help wanted (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
proxy.golang.org: github.com/crsh/citr
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.9%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.0 depends
  • RefManageR >= 0.14.2 imports
  • assertthat >= 0.1 imports
  • bibtex >= 0.4.2.2 imports
  • curl >= 1.1 imports
  • httr >= 1.3.1 imports
  • methods >= 3.0.0 imports
  • miniUI >= 0.1.1 imports
  • rstudioapi >= 0.6 imports
  • shiny >= 0.13.2 imports
  • shinyjs >= 1.0 imports
  • yaml >= 2.1.13 imports
  • testthat >= 1.0.2 suggests