In nealhaddaway/bibfix: Repair and enrich bibliographic data

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bibfix

bibfix is an R package and a Shiny app that helps users repair and enrich their bibliographic data. It does so through a suite of functions that request bibliographic data from API services including OpenAlex and The Lens.org. Repaired fields can include titles, abstract, unique identifiers (e.g. DOIs), publication years, etc. In addition, bibliographic records can be supplemented with additional information, including internal identifiers for common databases (e.g. The Lens.org, PubMed, Microsoft Academic) that facilitate deduplication, and information such as author affiliations and identifiers (e.g. ORCIDs).

The package is a work in progress and is part of the Evidence Synthesis Hackathon.

Here is a quick example of the workflow.

To install the latest version of the package:

remotes::install_github("nealhaddaway/bibfix")

The package is in active development so please make sure you always have the most up-to-date version.

We use synthesisr to read in a .ris file and we use functions in tidyverse for data wrangling and visualisations.

library(bibfix)
library(synthesisr)
library(tidyverse)

Read in a .ris file. synthesisr converts the .ris file to a dataframe.

refs<-synthesisr::read_refs(paste0(system.file(package="bibfix"),"/shiny-examples/bibfix/www/references.ris"))

First we can assess the "health" (how complete the file is) using the scan_file() function.

check_refs<-scan_file(refs)     

We can then plot out the percentage of references that have complete data across fields.

plot_health(check_refs) 

The repaired_refs() function searches on lens.org and OpenAlex to try and fill in missing (meta)data.

repaired_refs<-repair_refs(check_refs$refs)                      

scan_repaired<-scan_file(repaired_refs)

You can see that we have managed to add complete data for a further r scan_repaired$n_complete- check_refs$n_complete articles. We have added a further r scan_repaired$n_abstract- check_refs$n_abstract abstracts.

nealhaddaway/bibfix documentation built on Dec. 24, 2024, 7:43 p.m.