xciter

This package focuses solely on “extra” functions related to citeing bibliography items such as processing .bib files to get citation keys, processing BiBtex keys to get inline citations, etc. We are calling it “extra” because we rely heavily on rbbt and standard rmarkdown::render magic to almost everything we need to do. Some functions for rendering citation keys as inline references wrap calls to pandoc so that needs to be installed. If you have Rstudion you likely have it already.

This package deals with a few problems as follows:

• Provides a central place for us to keep an up to date NewGraphEnvironment.bib file representing our shared library. Can be found here path_bib <- system.file("extdata", "NewGraphEnvironment.bib", package = "xciter")
• Identify all citation keys in documents and confirm their presence in a specified .bib file.
• Highlight citation keys that do not match and suggest the closest matching keys from the .bib file.
• Provide workarounds for citation handling in interactive tables (DT) and other HTML outputs where standard citation rendering in R Markdown and Quarto may fail.

Installation

You can install the development version of xciter from GitHub with:

# install.packages("devtools")
pak::pkg_install("NewGraphEnvironment/xciter")

Example

This is a basic example of subbing citation keys for inline references within a table so that it can be rendered as is after the changes are made:

library(xciter)
## basic example code

path_bib <- system.file("extdata", "NewGraphEnvironment.bib", package = "xciter")
dat <- data.frame(
  id = 1:3,
  bib_keys = c(
    "Outside block quotes @busch_etal2011LandscapeLevelModela and in [@woll_etal2017SalmonEcological]",
    "This is many [@busch_etal2011LandscapeLevelModela; @woll_etal2017SalmonEcological; @kirsch_etal2014Fishinventorya]",
    "this is a failed key @key3"
  )
)
result <- xct_keys_to_inline_table_col(dat, col_format = "bib_keys", path_bib = path_bib)
print(result)
#>   id
#> 1  1
#> 2  2
#> 3  3
#>                                                                                             bib_keys
#> 1                    Outside block quotes Busch et al. (2011) and in (Woll, Albert, and Whited 2017)
#> 2 This is many (Busch et al. 2011; Woll, Albert, and Whited 2017; Kirsch, Buckwalter, and Reed 2014)
#> 3                                                                       this is a failed key (key3?)

This is a basic example of checking if the citation keys within a bookdown document are found within a specified .bib file.

key_missing <- xct_bib_keys_missing(path_bib, "kirsch_etal2014Fishinventory")
#> ! The following citations were not found in the BibTeX file:
#> [1] "kirsch_etal2014Fishinventory"

This is an example of how to search for the closest match for an unmatched key.

xct_keys_guess_match(key_missing, keys_bib = xct_bib_keys_extract(path_bib))
#>                    key_missing       key_missing_guess_match
#> 1 kirsch_etal2014Fishinventory kirsch_etal2014Fishinventorya