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Fill missed conflict-of-interest disclosures from PubMed

Source: R/rt_coi_pubmed.R
rt_fill_coi_pubmed.Rd

For rows of detector output where no conflict-of-interest statement was found (`is_coi_pred` is `FALSE`) but a PubMed ID is known, looks the article up with [rt_coi_pubmed()] and, when PubMed records a statement, sets `is_coi_pred` to `TRUE` and `coi_text` to that statement. A new `coi_source` column records where each disclosure came from.

Usage

rt_fill_coi_pubmed(data, api_key = Sys.getenv("ENTREZ_KEY"))

Arguments

data

A data frame with `pmid`, `is_coi_pred` and `coi_text` columns, such as the output of [rt_all_pmc()] or [rt_coi_pmc()].

api_key

An NCBI API key; defaults to the `ENTREZ_KEY` environment variable.

Value

`data` as a tibble with `is_coi_pred` and `coi_text` filled where PubMed has a statement, and `coi_source`: `"article"` (found in the full text), `"pubmed"` (filled from PubMed) or `NA` (none found).

Details

Note that the accuracy estimates in [rt_accuracy] describe the full-text detector alone; with this fallback the sensitivity is higher.

See also

[rt_coi_pubmed()]

Examples

# \donttest{
# Needs internet access.
res <- rt_all_pmc(system.file(
  "extdata", "PMID32171256-PMC7071725.xml", package = "rtransparency"
))
res <- try(rt_fill_coi_pubmed(res))
# }