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, RIS, or BIB 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
Review 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 and determine whether it
represents a true duplicate (press 1) or not (press 3). Save the output
to an object so you can use it in the next step.
True duplicates will have a “match” in the result column. Non duplicates with have a “no match” in the result column.
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 the results
of manual deduplication using the additional_pairs
argument. The rows where the result column = “match” will be considered
by ASySD to be additional duplicates.
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")