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Identify and extract all transparency indicators from a TXT file.

Source: R/rt_all.R
rt_all.Rd

Takes a plain-text article (a TXT file, or the text itself) and returns all ten indicators of transparency the package detects: conflicts of interest, funding, protocol registration, novelty, replication, data sharing, code sharing, generative-AI-use disclosure, open-access licensing and reporting-guideline use. The file is read once and every detector runs on the same text, with the same logic as the standalone plain-text functions ([rt_coi()], [rt_fund()], [rt_register()], [rt_novelty()], [rt_replication()], [rt_data_code()], [rt_ai()], [rt_oa()], [rt_reporting()]).

Usage

rt_all(filename = NULL, text = NULL)

Arguments

filename

The path to a TXT file as a string.

text

Alternatively, the article text itself as a character vector (for example the output of [rt_read_pdf()]). Supply `filename` or `text`.

Value

A one-row tibble: the file name (`article`) and PMID (`pmid`, the digits after "PMID" in the file name, `NA` if absent), then each indicator with the text that triggered it. The indicator columns carry the same names as in [rt_all_pmc()] (`is_coi_pred`, `is_fund_pred`, `is_register_pred`, `is_novelty_pred`, `is_replication_pred`, `is_open_data`, `is_open_code`, `is_ai_pred`, `is_open_access`, `is_reporting_pred`), so the result can be passed to [rt_summary()]. The pattern-function flags of the novelty and replication detectors are also returned; if one is `NA` it was not run. Unlike [rt_all_pmc()], `is_ai_pred` has no publication-year gate (see [rt_ai()]). `is_funded_pred` and `funding_text` are deprecated copies of the funding columns, kept for one release.

See also

[rt_all_pdf()] for a PDF, [rt_all_txt_dir()] for many files, and [rt_all_pmc()] for PMC XML.

Examples

# \donttest{
# Write a short example article to a temporary text file.
filepath <- file.path(tempdir(), "PMID00000000-PMC0000000.txt")
writeLines(c(
  "To our knowledge, this is the first study of its kind.",
  "Conflicts of interest: none declared.",
  "This work was supported by the National Institutes of Health (R01-000000).",
  "The protocol was registered at ClinicalTrials.gov (NCT00000000).",
  "All data and code are available at https://github.com/example/repo.",
  "We independently replicated the original analysis."
), filepath)

# Identify and extract indicators of transparency.
results_table <- rt_all(filepath)

# The same, from text already in memory.
results_table <- rt_all(text = readLines(filepath))
# }