Loading Citation Data
Begin by loading your citation data from an Endnote XML file using
the load_search() function. You can
specify alternative file formats such as CSV if needed.
citations <- load_search("systematic_search.xml", method="endnote")Automated deduplication
Remove duplicate citations automatically using the
dedup_citations function.
results <- dedup_citations(citations, merge_citations = TRUE)
#> formatting data...
#> identifying potential duplicates...
#> identified duplicates!
#> flagging potential pairs for manual dedup...
#> Joining with `by = join_by(duplicate_id.x, duplicate_id.y)`
#> 8948 citations loaded...
#> 3508 duplicate citations removed...
#> 5440 unique citations remaining!The dedup_citations function returns a list of two
dataframes by default. The first contains unique citations after
duplicates were removed automatically by ASySD. In most cases, this will
remove the vast majority of duplicates. There will likely be some
duplicates remaining which need manual review by a human (see next
step).
unique_citations <- results$uniqueManual deduplication
To address remaining duplicates, review potential pairs manually. You can examine them within R or export them to a CSV or Excel file for detailed inspection.
potential_duplicates <- results$manual_dedupReview the pairs using the manual_dedup_shiny()
function. This opens up and interactive shiny app to allow you to go
through each potential duplicate pair. Save the output to an object so
you can use it in the next step.
post_manual_review <- manual_dedup_shiny(potential_duplicates) Final Deduplication
Combine the results of automated and manual deduplication using the
dedup_citations_add_manual() function. Include any
additional duplicates you’ve identified in the
additional_pairs argument.
final_results <- dedup_citations_add_manual(unique_citations, additional_pairs = post_manual_review)Exporting Results
You can now write your results to a file for import into a reference manager or systematic review software
write_citations(final_results, type="txt", filename="citations.txt")