rt_all_pmc_dir: Identify transparency indicators across many PMC XML files.

In rtransparency: Identifies Indicators of Transparency

Identify transparency indicators across many PMC XML files.

Description

A batch wrapper around [rt_all_pmc()] for corpus-scale runs over a directory (or an explicit vector) of PMC XML files. It isolates per-file failures so a single malformed file cannot abort the run, shows a progress bar, can resume an interrupted run, and can run in parallel when the furrr package is installed.

Usage

rt_all_pmc_dir(
  dir,
  pattern = "\\.xml$",
  recursive = FALSE,
  remove_ns = FALSE,
  all_meta = FALSE,
  output = NULL,
  parallel = FALSE,
  progress = TRUE,
  chunk_size = 200L
)

Arguments

dir	A directory containing PMC XML files, or a character vector of file paths.
pattern	A regular expression for file names, used only when 'dir' is a single existing directory (default '"\.xml$"').
recursive	Whether to descend into subdirectories when 'dir' is a directory (default 'FALSE').
remove_ns, all_meta	Passed through to [rt_all_pmc()].
output	Optional path to a CSV file for incremental, resumable output (see Details). 'NULL' (default) keeps results in memory only.
parallel	Whether to process files in parallel via furrr (default 'FALSE').
progress	Whether to show a progress bar (default 'TRUE').
chunk_size	Number of files per write/flush when 'output' is set (default '200').

Details

When 'output' is supplied, results are written to that CSV in chunks as the run proceeds. Re-running with the same 'output' skips files already present in it and appends only the new results, so a long run can be resumed after an interruption. Each file is processed inside [tryCatch()]; a file that errors contributes a row with 'is_success = FALSE' rather than stopping the run.

Parallelism uses furrr's 'future_map()' and honors whatever 'future::plan()' is active (for example 'future::plan("multisession")'); with no plan it runs sequentially. Install furrr and future to use it.

Value

A [tibble][tibble::tibble] with one row per file, carrying the same columns as [rt_all_pmc()] (plus any rows read back from a pre-existing 'output'). Files that could not be processed have 'is_success = FALSE'.

See Also

[rt_all_pmc()] for a single file.

Examples

# Process every PMC XML in a directory (here, the bundled example file).
dir <- system.file("extdata", package = "rtransparency")
out <- tempfile(fileext = ".csv")
res <- rt_all_pmc_dir(dir, remove_ns = TRUE, output = out, parallel = FALSE)

rtransparency documentation built on July 1, 2026, 9:07 a.m.