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

In serghiou/rtransparent: 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.

Usage

rt_data_code_pmc(filename, remove_ns = T, 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	How specific should the extraction of text from the XML be? If "low" then this is a as sensitive as possible (it extracts all text). If "moderate", then it extracts all paragraphs. If "high", then it only extracts text from specific locations (footnotes, methods, supplements).

Value

A dataframe of results. It returns unique IDs of the article, whether this article is deemed a research article, whether it is deemed relevant to data or code, whether data or code was found, and if so, what the text that suggested the presence of data or code was. Takes a median of 200ms per article.

Examples

## Not run: 
# Path to PMC XML
filepath <- "../inst/extdata/00003-PMID26637448-PMC4737611.xml"

# Identify and extract meta-data and indicators of transparency
results_table <- rt_data_pmc(filepath, remove_ns = T)

## End(Not run)

serghiou/rtransparent documentation built on Dec. 26, 2024, 8:19 p.m.