findretractions

Installation

The findretractions package is a simple tool to help see if papers you have cited have associated retraction notices, erratums or expressions of concern. Currently, it can only find records on PubMed and CrossRef (using the RISmed and rcrossref packages); future versions may expand to other databases as well.

You can install the released version of findretractions using:

devtools::install_github("imaddowzimet/findretractions")

How to use it

check.bib() is the main function in the package. It takes as an input any BibTex file (.bib); .bib files can be exported from almost every reference manager software (like Zotero or Endnote). To export a BibTex file from Zotero, just select the library or collection you want to export, select File>Export Library…(or if it’s a collection, right click, and select Export Collection…), and choose the format “BibTex” in the pop-up window that appears:

Then just run check.bib with the link to the relevant file:

library(findretractions)
check.bib("Misc/My_Library.bib")
#> [1] "Warning: checking references now; expect a wait time of approximately 7.5 seconds"
#> 
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#> [[1]]
#> [1] "Check: Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. It may have been retracted"
#> 
#> [[2]]
#> [1] "Check: Genetic signatures of exceptional longevity in humans. It may have been retracted"
#> 
#> [[3]]
#> [1] "Check: Biological fabrication of cellulose fibers with tailored properties. There may be an associated erratum"

The function checks the references one by one, and is careful to not overload PubMed or Crossref with too many requests, so it may take some time to run. It returns a list of any flagged articles, or an empty list if it hasn’t found anything.

IMPORTANT: This function is mean to flag possible retractions, erratums or expressions of concern. Any articles it flags should be checked on PubMed, CrossRef and the publisher’s website directly, so that you can find the content of the notice, and be aware that it will not flag any notice not indexed on PubMed (and there are documented lags in when retraction notices get posted to PubMed; see Decullier E et al., 2014; there are similar issues for CrossRef). Right now, the Retraction Watch Database has the most up to date listings of retracted articles; unfortunately, as it doesn’t yet have an API, articles need to be searched for manually on their site.

Note: If you encounter an error that states something like ""application/json;charset=UTF-8" is not TRUE", you may have an older version of the rcrossref package, which seems to have a small bug. To fix this, reinstall the development version of rcrossref from Github:

remotes::install_github("ropensci/rcrossref")