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Calculate Phase Counts with Precision and Recall

Source: R/new_count_and_table.R
calculate_phase_records.Rd

This function calculates the distinct record counts, as well as screened and final record counts, for each citation source across different phases (e.g., "screened", "final"). It also calculates precision and recall metrics for each source.

Usage

calculate_phase_records(unique_citations, n_unique, db_colname)

Arguments

unique_citations

A data frame containing unique citations. It must include the columns cite_source, cite_label, and duplicate_id.

n_unique

A data frame containing counts of unique records. Typically filtered by specific criteria, such as cite_label == "search".

db_colname

The name of the column representing the citation source in the unique_citations data frame.

Value

A data frame with phase counts and calculated precision and recall for each citation source, including:

  • Distinct Records: The count of distinct records per source.

  • screened: The count of records in the "screened" phase.

  • final: The count of records in the "final" phase.

  • Precision: The precision metric calculated as final / Distinct Records.

  • Recall: The recall metric calculated as final / Total final records.

Details

The function starts by calculating the total distinct records, as well as the total "screened" and "final" records across all sources. It then calculates distinct counts for each source, followed by counts for "screened" and "final" records. Finally, it calculates precision and recall metrics and adds a total row summarizing these counts across all sources.

Examples

# Example usage with a sample dataset
unique_citations <- data.frame(
  cite_source = c("Source1", "Source2", "Source3"),
  cite_label = c("screened","screened", "final"),
  duplicate_id = c(1, 2, 3)
)
n_unique <- data.frame(
  cite_source = c("Source1", "Source2", "Source3"),
  unique = c(10, 20, 30)
)
calculate_phase_records(unique_citations, n_unique, "cite_source")
#> # A tibble: 4 × 6
#>   Source  Distinct_Records screened final Precision Recall
#>   <chr>              <int>    <dbl> <dbl>     <dbl>  <dbl>
#> 1 Source1                1        1     0       0        0
#> 2 Source2                1        1     0       0        0
#> 3 Source3                1        0     1     100      100
#> 4 Total                  3        2     1      33.3     NA