Checks DOIs against retraction databases to identify retracted publications. Uses OpenRetractions API to validate publication status and can optionally retrieve PubMed IDs. Includes DOI format validation, rate limiting, and robust error handling for reliable results.
Arguments
- data
The data as a data frame containing the DOI variable to check. Must have at least one column with DOI strings.
- doi
Column containing DOI strings to check for retractions. Supports multiple DOI formats including bare DOIs (10.1000/example), DOI URIs (doi:10.1000/example), and DOI URLs (https://doi.org/10.1000/example).
- database
Database to check for retractions. OpenRetractions is recommended as it provides comprehensive and up-to-date retraction information. RetractionWatch option currently uses OpenRetractions as fallback.
- pmid
If TRUE, attempts to retrieve corresponding PubMed IDs for valid DOIs using the rcrossref package. Requires internet connection and may increase processing time for large datasets.
Value
A results object containing:
results$todo | a html | ||||
results$summary | a table | ||||
results$details | a html | ||||
results$pmids | a preformatted |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$summary$asDF
as.data.frame(results$summary)
Examples
# \donttest{
# Example 1: Basic retraction check
data <- data.frame(
doi = c("10.1126/science.aac4716", "10.1038/nature12373", "10.1016/j.cell.2014.09.045")
)
result <- retracted(data = data, doi = "doi")
# Example 2: Include PubMed IDs
result_with_pmid <- retracted(
data = data,
doi = "doi",
pmid = TRUE
)
# Example 3: Using different database
result_rw <- retracted(
data = data,
doi = "doi",
database = "rw"
)
# }