Check for Missing Citation Keys in a BibTeX File

This function identifies citation keys provided in a list that are missing from a specified BibTeX file. It ensures the BibTeX file exists and processes the file to match the citation keys.

This function extracts all citation keys from a given BibTeX file.

This function attempts to find the closest matching citation keys for keys that are missing from a BibTeX file, based on string distance. Users can set a threshold for the maximum allowable distance for a match, optionally exclude rows where no matches are close enough, and choose the string distance calculation method.

Usage

xct_bib_keys_missing(path_bib, citations)

xct_bib_keys_extract(path_bib)

xct_keys_guess_match(
  keys_missing,
  keys_bib,
  stringdist_threshold = 15,
  stringdist_method = "dl",
  no_match_rows_include = FALSE
)

Arguments

path_bib

A file path to the bibliography file (.bib) used for citation keys. Defaults to "references.bib" in the current working directory.

keys_missing

character A vector of citation keys that are missing from the BibTeX file. Typically obtained using xct_bib_keys_missing().

keys_bib

character A vector of citation keys extracted from the BibTeX file. Typically obtained using xct_bib_keys_extract().

stringdist_threshold

numeric The maximum allowable string distance for a match to be considered valid. This value is passed to [stringdist::stringdist()] for the specified method. Distances are non-negative numeric values where smaller values indicate greater similarity. For short strings (5-10 characters), use 1-3; for medium strings (10-20 characters), use 3-7; and for longer strings (>20 characters), use 7-15. Default is 15. Interestingly, we see some accurate matches at 25 however we also get mismatches when we go this high which could result in incorrect citations if we find replace those!!

stringdist_method

character The method used by [stringdist::stringdist()] to calculate string distances. Options include "osa" (Optimal String Alignment, default), "lv" (Levenshtein), "dl" (Damerau-Levenshtein), "jw" (Jaro-Winkler), and others. See [stringdist::stringdist()] documentation for details. Default is "dl".

no_match_rows_include

logical Whether to include rows for keys with no valid matches in the output. Default is FALSE, which excludes such rows.

keys

character A vector of citation keys to check for in the BibTeX file.

Value

A vector of citation keys missing from the BibTeX file. Returns an empty vector if all citation keys are found.

A character vector of citation keys extracted from the BibTeX file.

A data frame with two columns:

key_missing

The missing citation keys.

key_missing_guess_match

The guessed closest matching citation keys (or NA if no valid match is found).

If no_match_rows_include = FALSE, rows with no valid matches are excluded.

See also

xct_bib_keys_missing(), xct_bib_keys_extract(), stringdist::stringdist()

Other cite: xct_assemble(), xct_format(), xct_format_single(), xct_keys_extract(), xct_keys_to_inline(), xct_keys_to_xref()

Examples

if (FALSE) { # \dontrun{
path_bib <- system.file("extdata", "references.bib", package = "xciter")
citations <- c("Smith2020", "Jones2019")
xct_bib_keys_missing(path_bib, citations)
} # }
# Path to the example BibTeX file
path_bib <- system.file("extdata", "references.bib", package = "xciter")

# Define the citation keys to check
keys <- c("busch_etal2011LandscapeLevelModel",
          "kirsch_etal2014Fishinventoryb",
          "test2001")

# Extract keys from the BibTeX file
keys_bib <- xct_bib_keys_extract(path_bib)

# Identify missing keys
keys_missing <- xct_bib_keys_missing(path_bib, keys)
#> ! The following citations were not found in the BibTeX file:
#> [1] "busch_etal2011LandscapeLevelModel" "kirsch_etal2014Fishinventoryb"    
#> [3] "test2001"                         

# Guess matches for missing keys with a string distance threshold and method
xct_keys_guess_match(keys_missing, keys_bib)
#>                         key_missing            key_missing_guess_match
#> 1 busch_etal2011LandscapeLevelModel busch_etal2011LandscapeLevelModela
#> 2     kirsch_etal2014Fishinventoryb       kirsch_etal2014Fishinventory
#> 3                          test2001                      data_fish_obs