Package index • rtransparency

Package

rtransparency rtransparency-package: rtransparency: Identify indicators of transparency in the biomedical literature

Detect every indicator in one pass, for one file or a whole corpus.

rt_all(): Identify and extract all transparency indicators from a TXT file.
rt_all_pdf(): Identify and extract all transparency indicators from a PDF file.
rt_all_pmc(): Identify and extract all transparency indicators from a PMC XML.
rt_all_pmc_dir(): Identify transparency indicators across many PMC XML files.
rt_all_txt_dir(): Identify transparency indicators across many TXT or PDF files.

One detector per indicator, for PMC JATS XML files.

rt_coi_pmc(): Identify and extract Conflicts of Interest (COI) statements in PMC XML files.
rt_fund_pmc(): Identify and extract Funding statements in PMC XML files.
rt_register_pmc(): Identify and extract Conflicts of Interest statements in PMC XML files.
rt_novelty_pmc(): Identify and extract novelty claims in PMC XML files.
rt_replication_pmc(): Identify and extract replication components in PMC XML files.
rt_data_code_pmc(): Identify and extract Data and Code sharing from PMC XML files.
rt_data_code_pmc_list(): Identify and extract Data and Code sharing from a list of PMC XML files.
rt_ai_pmc(): Identify disclosure of generative-AI use from a PMC XML file.
rt_oa_pmc(): Identify the open-access status and reuse license of a PMC XML file.
rt_reporting_pmc(): Identify use of a reporting guideline from a PMC XML file.

One detector per indicator, for plain-text (PDF-derived) files.

rt_coi(): Identify and extract Conflicts of Interest (COI) statements in TXT files.
rt_fund(): Identify and extract Funding statements in TXT files.
rt_register(): Identify and extract Registration statements in TXT files.
rt_novelty(): Identify whether a study claims novelty in TXT files.
rt_replication(): Identify whether a study includes a replication component in TXT files.
rt_data_code(): Identify and extract Data and Code statements in TXT files.
rt_ai(): Identify disclosure of generative-AI use from a TXT file.
rt_oa(): Identify the open-access status and reuse license from a TXT file.
rt_reporting(): Identify use of a reporting guideline from a TXT file.

Download PMC full text, convert identifiers and read PDFs.

Tagged JATS metadata read directly, not detected from prose.

rt_meta_pmc(): Extract article metadata from a PMC XML file.
rt_authors_pmc(): Author identifiers and contribution roles from a PMC XML file.
rt_funders_pmc(): Funders, funder identifiers and award numbers from a PMC XML file.

Go beyond presence of a statement, using registries, PubMed and the web.

rt_trial_ids(): Extract trial and review registration identifiers from text
rt_registration_timing(): Check whether ClinicalTrials.gov registrations were prospective
rt_coi_pubmed(): Fetch conflict-of-interest statements recorded in PubMed
rt_fill_coi_pubmed(): Fill missed conflict-of-interest disclosures from PubMed
rt_check_links(): Check whether extracted data and code links resolve

Detectors not yet validated against hand labels; not part of rt_all_pmc().

rt_ethics_pmc(): Identify ethics approval and informed consent statements (experimental)
rt_ethics(): Identify ethics approval and informed consent statements in text (experimental)

Corpus-level prevalence, per-article scores and plots.

rt_summary(): Summarize transparency indicators across a corpus of articles
rt_score(): Count the transparency indicators met by each article
rt_plot(): Plot transparency indicators