Identifies Indicators of Transparency

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Documentation for package ‘rtransparency’ version 1.2.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

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rtransparency-package	rtransparency: Identify indicators of transparency in the biomedical literature
rtransparency	rtransparency: Identify indicators of transparency in the biomedical literature
rt_accuracy	Detector accuracy estimates
rt_accuracy_2021	Published 2021 detector accuracy estimates
rt_ai	Identify disclosure of generative-AI use from a TXT file.
rt_ai_pmc	Identify disclosure of generative-AI use from a PMC XML file.
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.
rt_authors_pmc	Author identifiers and contribution roles from a PMC XML file.
rt_check_links	Check whether extracted data and code links resolve
rt_coi	Identify and extract Conflicts of Interest (COI) statements in TXT files.
rt_coi_pmc	Identify and extract Conflicts of Interest (COI) statements in PMC XML files.
rt_coi_pubmed	Fetch conflict-of-interest statements recorded in PubMed
rt_convert_ids	Convert article identifiers with the PMC ID Converter
rt_data_code	Identify and extract Data and Code statements in TXT 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_demo	Simulated transparency indicators for a corpus of articles
rt_ethics	Identify ethics approval and informed consent statements in text (experimental)
rt_ethics_pmc	Identify ethics approval and informed consent statements (experimental)
rt_fetch_pmc	Download PubMed Central full-text XML
rt_fill_coi_pubmed	Fill missed conflict-of-interest disclosures from PubMed
rt_fund	Identify and extract Funding statements in TXT files.
rt_funders_pmc	Funders, funder identifiers and award numbers from a PMC XML file.
rt_fund_pmc	Identify and extract Funding statements in PMC XML files.
rt_meta_pmc	Extract article metadata from a PMC XML file.
rt_novelty	Identify whether a study claims novelty in TXT files.
rt_novelty_pmc	Identify and extract novelty claims in PMC XML files.
rt_oa	Identify the open-access status and reuse license from a TXT file.
rt_oa_pmc	Identify the open-access status and reuse license of a PMC XML file.
rt_plot	Plot transparency indicators
rt_read_pdf	Convert a PDF file to text.
rt_register	Identify and extract Registration statements in TXT files.
rt_register_pmc	Identify and extract Conflicts of Interest statements in PMC XML files.
rt_registration_timing	Check whether ClinicalTrials.gov registrations were prospective
rt_replication	Identify whether a study includes a replication component in TXT files.
rt_replication_pmc	Identify and extract replication components in PMC XML files.
rt_reporting	Identify use of a reporting guideline from a TXT file.
rt_reporting_pmc	Identify use of a reporting guideline from a PMC XML file.
rt_score	Count the transparency indicators met by each article
rt_summary	Summarize transparency indicators across a corpus of articles
rt_trial_ids	Extract trial and review registration identifiers from text