## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", eval = FALSE)

## ----setup--------------------------------------------------------------------
# library(retraction)

## -----------------------------------------------------------------------------
# retraction::retraction_knit_check(bib = "references.bib", on = "flagged",
#                                   action = "error")

## -----------------------------------------------------------------------------
# # Rscript -e 'retraction::retraction_main()' --fail-on=flagged,unchecked paper.bib
# scan <- retraction_scan("paper.bib")
# scan$n_flagged

## -----------------------------------------------------------------------------
# system.file("actions", "action.yml", package = "retraction")

## -----------------------------------------------------------------------------
# check_included_studies(c("10.1016/S0140-6736(97)11096-0",
#                          "10.1136/bmj.331.7531.1512"))

## -----------------------------------------------------------------------------
# res <- check_file("review.bib")
# retraction_watch_save(res, "my-review")
# 
# # ... weeks later ...
# newly <- retraction_watch_diff(check_file("review.bib"), "my-review")

## -----------------------------------------------------------------------------
# list_backends()
# check_dois("10.1016/S0140-6736(97)11096-0",
#            sources = c("xera", "europepmc", "ncbi"))
# compare_sources(check_dois("10.1126/science.aac4716", sources = "all"))

## -----------------------------------------------------------------------------
# res <- check_file("paper.bib")
# explain_result(res)                 # a sentence per reference
# exposure_score(res)                 # flagged rate with denominators
# export_result(res, "results.xlsx")  # or .csv / .json
# annotate_bib("paper.bib", res)      # write back a marked-up bibliography

## -----------------------------------------------------------------------------
# retraction_sync()
# check_file("paper.bib", offline = TRUE)
# snapshot_info()
# 
# # Parallelism for large reference lists (set a future plan):
# # future::plan("multisession"); check_dois(many_dois)
# 
# p <- retraction_snapshot_parquet()
# arrow::open_dataset(p)

## -----------------------------------------------------------------------------
# # _targets.R
# library(targets)
# list(
#   tar_target(bib, "paper.bib", format = "file"),
#   tar_target(checked, retraction::check_file(bib)),
#   tar_target(gate, if (nrow(retraction::retracted(checked, "flagged")))
#                      stop("retracted references present") else TRUE)
# )