This function deduplicates citation data

Usage

dedup_citations(
  raw_citations,
  manual_dedup = TRUE,
  merge_citations = TRUE,
  keep_source = NULL,
  keep_label = NULL,
  extra_merge_fields = NULL,
  show_unknown_tags = TRUE,
  user_input = NA
)

Arguments

raw_citations: A dataframe containing duplicate ciations
manual_dedup: Logical value. Do you want to retrieve dataframe for manual deduplication?
merge_citations: Logical value. Do you want to merge matching citations?
keep_source: Character vector. Selected citation source to preferentially retain in the dataset as the unique record
keep_label: Selected citation label to preferentially retain in the dataset as the unique record
extra_merge_fields: Add additional fields to merge, output will be similar to the label, source, and record_id columns with commas between each merged value
show_unknown_tags: When a label, source, or other merged field is missing, do you want this to show as "unknown"?
user_input: Do you want to proceed if important columns are missing? 1-yes; 2-no

Value

A list of 2 dataframes - unique citations and citations to be manually deduplicated if option selected

Details

The following fields will be used in raw_citations (if provided): record_id, author, year, journal, doi, title, pages, volume, number, abstract, isbn, label, source

Examples


# Perform deduplication
result <- dedup_citations(citations_df, keep_source="Embase")
#> formatting data...
#> identifying potential duplicates...
#> identified duplicates!
#> flagging potential pairs for manual dedup...
#> Joining with `by = join_by(duplicate_id.x, duplicate_id.y)`
#> 1001 citations loaded...
#> 392 duplicate citations removed...
#> 609 unique citations remaining!

# View unique citations
head(result$unique)
#> # A tibble: 6 × 16
#>   duplicate_id author     year  journal doi   title pages volume number abstract
#>   <chr>        <chr>      <chr> <chr>   <chr> <chr> <chr> <chr>  <chr>  <chr>   
#> 1 1018         Della-Mor… 2012  Pharma… 10.2… Gene… 1741… 13     15     A subth…
#> 2 1107         Downey J.… 2008  Expert… 10.1… Free… 589-… 6      5      NA      
#> 3 1127         Duan D. Y… 2005  Acta P… 10.1… Func… 265-… 26     3      In comp…
#> 4 1184         Eskildsen… 1996  Ann N … 10.1… Expl… 210-… 793    NA     NA      
#> 5 1288         Fryer R. … 2001  Am J P… 10.1… Esse… H134… 280    3      Stimula…
#> 6 1290         Fryer R. … 2001  Basic … 10.1… ERK … 136-… 96     2      Opioids…
#> # ℹ 6 more variables: isbn <chr>, secondary_title <chr>, label <chr>,
#> #   url <chr>, source <chr>, record_ids <chr>