rt_data_code_pmc: Identify and extract Data and Code sharing from PMC XML...

In rtransparency: Identifies Indicators of Transparency

Identify and extract Data and Code sharing from PMC XML files.

Description

Takes a PMC XML file and returns data related to the presence of Data or Code, including whether Data or Code have been shared. If Data or Code exist, it will extract the relevant text for each. Detection is performed by the native detector (.detect_data_code); the package no longer depends on oddpub or tokenizers.

Usage

rt_data_code_pmc(filename, remove_ns = TRUE, specificity = "low")

Arguments

filename	The filename of the XML file to be analyzed as a string.
remove_ns	TRUE if an XML namespace exists, else FALSE (default).
specificity	Retained for backward compatibility; it no longer changes the result. The native detector extracts a fixed, broad set of article text (body paragraphs and titles, back matter, footnotes and supplements) and applies repository, accession and availability-statement patterns.

Value

A dataframe of results: the unique IDs of the article, whether data or code sharing was found (is_open_data, is_open_code), the statement text that triggered each detection (open_data_statements, open_code_statements) and the persistent identifiers and URLs of what was shared (open_data_links, open_code_links). The links are the DOIs (as doi.org URLs), repository URLs and database accessions (as identifiers.org prefix:accession) extracted from the statements, separated by " ; ".

Examples

# Path to PMC XML
filepath <- system.file(
  "extdata", "PMID32171256-PMC7071725.xml", package = "rtransparency"
)

# Identify and extract indicators of data and code sharing
results_table <- rt_data_code_pmc(filepath, remove_ns = TRUE)

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