rt_all_pmc: Identify and extract statements of COI, Funding and...

In serghiou/rtransparent: Identifies indicators of transparency

Identify and extract statements of COI, Funding and Registration.

Description

Takes a PMC XML and returns relevant meta-data, as well as whether any statements of Conflicts of Interest (COI), Funding or Protocol Registration. If any such statements are found, it also extracts the relevant text.

Usage

rt_all_pmc(filename, remove_ns = F, all_meta = F)

Arguments

filename	The name of the PMC XML as a string.
remove_ns	TRUE if an XML namespace exists, else FALSE (default).
all_meta	TRUE extracts all meta-data, FALSE extracts some (default).

Value

A dataframe of results. It returns the unique identifiers of the article, whether each of 3 indicators of transparency (COI, Funding or Registration) was identified, the relevant text identified, whether it was identified through a dedicated XML tag (such variables include "pmc" in their name, e.g. “fund_pmc_source”) and whether each labelling function identified relevant text or not. The labeling functions are returned to add flexibility in how this package is used; for example, future definitions of Registration may differ from the one we used. If a labelling function returns NA it means that it was not run.

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_all_pmc(filepath, remove_ns = T, all_meta = T)

## End(Not run)

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