Manage Bibliography

Manage Bibliography

Create, merge, dedup BibTeX bib files via R. Full lifecycle: parse existing .bib → structured R, gen new entries from identifiers (DOI, ISBN, arXiv ID), merge multi bibs w/ intelligent dedup, export clean consistent .bib.

Use When

• New .bib for R Markdown / Quarto project
• Merge bibs from multi collaborators / sources
• Dedup .bib grown by copy-paste accumulation
• Gen BibTeX entries programmatically from DOIs / identifiers
• Clean + standardize existing .bib (consistent keys, sorted fields)

In

• Req: Path to ≥1 .bib files, or list of DOIs/ISBNs/arXiv IDs
• Opt: Output .bib path (default: references.bib)
• Opt: Dedup strategy (doi, title, both; default: both)
• Opt: Sort order (author, year, key; default: key)
• Opt: Key gen pattern (default: AuthorYear)

Do

Step 1: Install + Load Pkgs

required_packages <- c("RefManageR", "bibtex", "stringdist")
missing <- required_packages[!vapply(required_packages, requireNamespace,
                                     logical(1), quietly = TRUE)]
if (length(missing) > 0) install.packages(missing)

library(RefManageR)

→ All pkgs load w/o errs.

If err: RefManageR fails → check curl + xml2 sys libs avail. Ubuntu: sudo apt install libcurl4-openssl-dev libxml2-dev.

Step 2: Parse Existing .bib

bib <- RefManageR::ReadBib("references.bib", check = FALSE)
message(sprintf("Parsed %d entries from references.bib", length(bib)))

# Inspect structure
print(bib[1:3])

# Access fields programmatically
keys <- names(bib)
years <- vapply(bib, function(x) x$year %||% NA_character_, character(1))

→ BibEntry obj w/ all entries. Count matches @article{, @book{, etc blocks.

If err: Parse fails → check unmatched braces / invalid UTF-8. Fallback: bibtex::read.bib() w/ stricter parsing.

Step 3: Gen Entries from Identifiers

# From DOI
entry_doi <- RefManageR::GetBibEntryWithDOI("10.1093/bioinformatics/btz848")

# From a vector of DOIs
dois <- c("10.1093/bioinformatics/btz848", "10.1038/s41586-020-2649-2")
entries <- do.call(c, lapply(dois, function(d) {
  tryCatch(
    RefManageR::GetBibEntryWithDOI(d),
    error = function(e) {
      warning(sprintf("Failed to fetch DOI %s: %s", d, e$message))
      NULL
    }
  )
}))
entries <- Filter(Negate(is.null), entries)

→ BibEntry objs w/ complete metadata (title, author, journal, year, DOI) per resolved identifier.

If err: DOI resolution → CrossRef API. Failed → check connectivity + DOI valid. Rate limiting for large batches → Sys.sleep(1) between reqs.

Step 4: Merge Multi Bibs

bib1 <- RefManageR::ReadBib("project_a.bib", check = FALSE)
bib2 <- RefManageR::ReadBib("project_b.bib", check = FALSE)

# Simple merge
merged <- c(bib1, bib2)
message(sprintf("Merged: %d + %d = %d entries (before dedup)",
                length(bib1), length(bib2), length(merged)))

→ Combined BibEntry obj w/ entries from both files.

Step 5: Dedup Entries

deduplicate_bib <- function(bib, method = "both") {
  n_before <- length(bib)
  keys_to_remove <- c()

  for (i in seq_along(bib)) {
    if (names(bib)[i] %in% keys_to_remove) next
    for (j in seq(i + 1, length(bib))) {
      if (j > length(bib)) break
      if (names(bib)[j] %in% keys_to_remove) next

      is_dup <- FALSE
      if (method %in% c("doi", "both")) {
        doi_i <- bib[[i]]$doi %||% ""
        doi_j <- bib[[j]]$doi %||% ""
        if (nzchar(doi_i) && nzchar(doi_j) && tolower(doi_i) == tolower(doi_j)) {
          is_dup <- TRUE
        }
      }
      if (!is_dup && method %in% c("title", "both")) {
        title_i <- tolower(gsub("[^a-z0-9 ]", "", tolower(bib[[i]]$title %||% "")))
        title_j <- tolower(gsub("[^a-z0-9 ]", "", tolower(bib[[j]]$title %||% "")))
        if (nzchar(title_i) && nzchar(title_j)) {
          sim <- 1 - stringdist::stringdist(title_i, title_j, method = "jw")
          if (sim > 0.95) is_dup <- TRUE
        }
      }
      if (is_dup) keys_to_remove <- c(keys_to_remove, names(bib)[j])
    }
  }

  if (length(keys_to_remove) > 0) {
    bib <- bib[!names(bib) %in% keys_to_remove]
  }
  message(sprintf("Deduplication: %d -> %d entries (%d duplicates removed)",
                  n_before, length(bib), n_before - length(bib)))
  bib
}

merged <- deduplicate_bib(merged, method = "both")

→ Dup entries removed. Count of removed dups printed.

If err: Title comparison too aggressive (removing non-dups) → raise threshold > 0.95 or switch method = "doi" only.

Step 6: Sort + Export

# Sort by citation key
sorted_bib <- sort(merged, sorting = "nyt")  # name-year-title

# Export to .bib file
RefManageR::WriteBib(sorted_bib, file = "references.bib", biblatex = FALSE)
message(sprintf("Wrote %d entries to references.bib", length(sorted_bib)))

→ Clean .bib on disk w/ consistent format, one entry per block, sorted alphabetically by key.

If err: WriteBib encoding issues → ensure R locale supports UTF-8: Sys.setlocale("LC_ALL", "en_US.UTF-8").

Check

• Output .bib parses w/o errs: RefManageR::ReadBib("references.bib")
• Entry count matches expectations (input - dups)
• No dup DOIs remain: all DOIs in output unique
• All entries have citation key
• Required fields per entry type (author, title, year min)
• File valid BibTeX (test w/ bibtex::read.bib())

Traps

• Encoding issues: Latin-1 accents break UTF-8 parsers. Convert first: iconv -f ISO-8859-1 -t UTF-8 old.bib > new.bib
• Unmatched braces: Single missing } silently drops entries. Validate balance before parsing large.
• DOI rate limiting: CrossRef throttles unauthenticated. Set polite email w/ RefManageR::BibOptions(check.entries = FALSE) + batch reqs.
• Key collisions: Merging files w/ dup keys (both have Smith2020) silently overwrites. Regen keys after merge.
• LaTeX in titles: Titles w/ {DNA} / $\alpha$ need careful handling. RefManageR preserves but downstream may strip.

→

• format-citations — format bib entries → styled citations
• validate-references — verify completeness + DOI resolution
• ../reporting/format-apa-report — APA-formatted reports using bibs
• ../r-packages/write-vignette — pkg vignettes citing refs