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Export deduplicated citations with source data as CSV file

Source: R/export.R
export_csv.Rd

This function saves deduplicated citations as a CSV file for further analysis and/or reporting. Metadata can be separated into one column per source, label or string, which facilitates analysis. Note that existing files are overwritten without warning.

Usage

export_csv(
  unique_citations,
  filename,
  fields = "full",
  separate = NULL,
  trim_abstracts = 32000,
  manual_dedup_complete = FALSE
)

Arguments

unique_citations

Dataframe with unique citations, resulting from dedup_citations()

filename

Name (and path) of file, should end in .csv

fields

Controls which columns are included. Use "full" (default) to export all columns (required for reimport into CiteSource via reimport_csv()); "standard" to export core bibliographic fields plus cite_source, cite_label, and cite_string (suitable for import into RELApp or other screening tools); or a character vector of column names for a custom selection. Note that exports other than "full" cannot be reimported into CiteSource.

separate

Character vector indicating which (if any) of cite_source, cite_string and cite_label should be split into separate columns to facilitate further analysis.

trim_abstracts

Some databases may return full-text that is misidentified as an abstract. This inflates file size and may lead to issues with Excel, which cannot deal with more than 32,000 characters per field. Therefore, the default is to trim very long abstracts to 32,000 characters. Set a lower number to reduce file size, or NULL to retain abstracts as they are.

manual_dedup_complete

Logical. Records, in a manual_dedup_complete column, whether manual deduplication has been completed for this set (default FALSE). Set TRUE after confirming manual pairs with dedup_citations_add_manual(). This flag is read back by reimport_csv() and lets later steps know whether candidate pairs still need review. Only written when fields = "full".

Value

No return value, called for side effects. Saves the deduplicated citations as a 'CSV' file to the specified location.

Examples

if (interactive()) {
  # Load example data from the package
  examplecitations_path <- system.file("extdata", "examplecitations.rds", package = "CiteSource")
  examplecitations <- readRDS(examplecitations_path)
  dedup_results <- dedup_citations(examplecitations, merge_citations = TRUE)
  export_csv(dedup_results, tempfile(fileext = ".csv"), separate = "cite_source")
  # Standard export for RELApp / screening tools (not reimportable into CiteSource):
  export_csv(dedup_results, tempfile(fileext = ".csv"), fields = "standard")
}