Package: rtransparency 1.0.0

Ahmad Sofi-Mahmudi

rtransparency: Identifies Indicators of Transparency

Use this package to identify indicators of transparency within the published literature. It can identify and extract text related to indicators of transparency from specifically formatted TXT files and from PMC XML files (i.e. XML files downloaded from the PubMed Central). It builds on the original 'rtransparent' tool of Serghiou et al. (2021) <doi:10.1371/journal.pbio.3001107>.

Authors:Stylianos Serghiou [aut], Ahmad Sofi-Mahmudi [cre, aut]

rtransparency_1.0.0.tar.gz
rtransparency_1.0.0.tar.gz(r-4.7-any)rtransparency_1.0.0.tar.gz(r-4.6-any)
rtransparency_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rtransparency/json (API)

# Install 'rtransparency' in R:
install.packages('rtransparency', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/choxos/rtransparency/issues

Pkgdown/docs site:https://choxos.github.io

Datasets:
  • rt_accuracy - Detector accuracy estimates
  • rt_demo - Simulated transparency indicators for a corpus of articles

On CRAN:

Conda:

3.30 score 7 scripts 23 exports 30 dependencies

Last updated from:f791c3cb6f. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK154
source / vignettesOK185
linux-release-x86_64OK148
wasm-releaseOK126

Exports:rt_airt_ai_pmcrt_allrt_all_pmcrt_all_pmc_dirrt_coirt_coi_pmcrt_data_codert_data_code_pmcrt_data_code_pmc_listrt_fundrt_fund_pmcrt_meta_pmcrt_noveltyrt_novelty_pmcrt_plotrt_read_pdfrt_registerrt_register_pmcrt_replicationrt_replication_pmcrt_scorert_summary

Dependencies:bitbit64clicliprcpp11crayondplyrgenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrrlangstringistringrtibbletidyselecttzdbutf8vctrsvroomwithrxml2

Detecting disclosure of generative-AI use
What this indicator captures | The 2023 year gate | In the all-indicators output | Across a corpus | Notes on precision
Rendered fromai-disclosure.Rmdusingknitr::rmarkdown

Last update: 2026-07-01
Started: 2026-07-01

Introduction to rtransparency
Overview | How detection works | Article parsing | Rule-based detection | Languages | Usage: PMC XML | All indicators at once | Individual indicators | Data and code sharing | AI-use disclosure | Usage: TXT files | Processing many articles | Summarizing a corpus | Downloading PMC XML | Validation | Naming convention and dependencies
Rendered fromrtransparency.Rmdusingknitr::rmarkdown

Last update: 2026-07-01
Started: 2026-07-01

Scope and limitations
What the indicators mean | Known limitations | Output schema | Linking to FAIR assessment
Rendered fromscope-and-limitations.Rmdusingknitr::rmarkdown

Last update: 2026-07-01
Started: 2026-07-01

Summarizing transparency across a corpus
From one article to many | Prevalence of each indicator | Correcting for detector error | How many practices per article | Subgroups | Plots | Putting it together
Rendered fromtransparency-summary.Rmdusingknitr::rmarkdown

Last update: 2026-07-01
Started: 2026-07-01

Readme and manuals

Help Manual

Help pageTopics
rtransparency: Identify indicators of transparency in the biomedical literaturertransparency-package rtransparency
Detector accuracy estimatesrt_accuracy
Identify disclosure of generative-AI use from a TXT file.rt_ai
Identify disclosure of generative-AI use from a PMC XML file.rt_ai_pmc
Identify and extract transparency statements from a TXT file.rt_all
Identify and extract all transparency indicators from a PMC XML.rt_all_pmc
Identify transparency indicators across many PMC XML files.rt_all_pmc_dir
Identify and extract Conflicts of Interest (COI) statements in TXT files.rt_coi
Identify and extract Conflicts of Interest (COI) statements in PMC XML files.rt_coi_pmc
Identify and extract Data and Code statements in TXT files.rt_data_code
Identify and extract Data and Code sharing from PMC XML files.rt_data_code_pmc
Identify and extract Data and Code sharing from a list of PMC XML files.rt_data_code_pmc_list
Simulated transparency indicators for a corpus of articlesrt_demo
Identify and extract Funding statements in TXT files.rt_fund
Identify and extract Funding statements in PMC XML files.rt_fund_pmc
Extract article metadata from a PMC XML file.rt_meta_pmc
Identify whether a study claims novelty in TXT files.rt_novelty
Identify and extract novelty claims in PMC XML files.rt_novelty_pmc
Plot transparency indicatorsrt_plot
Convert a PDF file to text.rt_read_pdf
Identify and extract Registration statements in TXT files.rt_register
Identify and extract Conflicts of Interest statements in PMC XML files.rt_register_pmc
Identify whether a study includes a replication component in TXT files.rt_replication
Identify and extract replication components in PMC XML files.rt_replication_pmc
Count the transparency indicators met by each articlert_score
Summarize transparency indicators across a corpus of articlesrt_summary