rt_accuracy: Detector accuracy estimates

In rtransparency: Identifies Indicators of Transparency

Detector accuracy estimates

Description

Sensitivity and specificity estimates for each transparency detector, used by [rt_summary()] to correct an apparent prevalence for detector error (the Rogan-Gladen correction).

Usage

rt_accuracy

Format

A tibble with 7 rows and 5 columns:

variable

Indicator column name, as returned by [rt_all_pmc()].

label

Human-readable indicator name.

sensitivity

Detector sensitivity (true-positive rate), 0-1.

specificity

Detector specificity (true-negative rate), 0-1.

source

Where the estimate comes from.

Details

For conflicts of interest, funding and protocol registration these are the published, importance-weighted validation values of Serghiou et al. (2021); the detectors for these indicators are essentially those validated in the paper. For data and code sharing the detector is implemented natively in this package (it no longer wraps ‘oddpub'), so the package’s reproducible benchmark and regression estimates are used instead (see 'inst/benchmark'). These data/code estimates are not an untouched external validation of the native detector; supply your own values to [rt_summary()] via its 'accuracy' argument when you have study-specific or externally validated estimates. Novelty's estimate comes from a maintainer-built hand-labeled gold set (see ‘inst/benchmark/results_novelty_replication.md'). Replication’s sensitivity comes from a 111-positive replication-enriched validation (see 'inst/benchmark/results_replication_enriched.md'), with the specificity from the 2023 1000-article sample. AI-use disclosure is not included (its prevalence is too low in unselected literature for a stable estimate), so [rt_summary()] reports it uncorrected.

Source

Serghiou S, Contopoulos-Ioannidis DG, Boyack KW, Riedel N, Wallach JD, Ioannidis JPA (2021). Assessment of transparency indicators across the biomedical literature: How open is open? PLOS Biology 19(3): e3001107. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1371/journal.pbio.3001107")}. Data and code values: this package's reproducible benchmark and regression estimates ('inst/benchmark/results_data_code.md').

See Also

[rt_summary()]

rtransparency documentation built on July 1, 2026, 9:07 a.m.