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

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 = NULL)

Arguments

filename: The filename of the XML file to be analyzed as a string.
remove_ns: Ignored since version 1.2.0 and kept for backward compatibility. Default XML namespaces are now always removed, so a namespaced PMC XML file gives the same result as a plain one.
specificity: Deprecated and ignored (it has not changed the result since the native detector replaced oddpub); supplying it gives a warning, and it will be removed in a future release. 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 " ; ". has_das records whether the article has a data-availability section (tagged, or titled as such) and das_text holds its text: having the statement is itself a reporting indicator, separate from whether data were actually shared (a statement can say data are available only on request).

Examples

# \donttest{
# 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)
# }