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Check whether extracted data and code links resolve

Source: R/data_code.R
rt_check_links.Rd

Takes the links extracted by the data and code detectors (the `open_data_links` and `open_code_links` columns of [rt_data_code_pmc()], [rt_all_pmc()] or [rt_data_code()]) and checks whether each one resolves, following redirects. A shared-data statement whose link is dead is weaker evidence of sharing than one whose link works, which availability-statement indicators alone cannot tell apart.

Usage

rt_check_links(links, timeout = 10)

Arguments

A character vector of links; elements holding several links separated by `" ; "` (as the detectors return them) are split.

timeout

Seconds to wait for each server.

Value

A tibble with one row per unique link: the `link`, the `url` checked, the HTTP `status` (`NA` when the server could not be reached), `is_ok` (a status below 400) and the `error` message when unreachable.

Details

DOIs are checked through `https://doi.org/`, and database accessions in identifiers.org `prefix:accession` form through `https://identifiers.org/`. Only the response headers are requested. Some servers refuse automated requests (status 403) or header-only requests (405) although the page exists, so a failing status is a prompt to look, not proof of a dead link.

See also

[rt_data_code_pmc()]

Examples

# \donttest{
# Needs internet access; unreachable links are reported, not errors.
res <- rt_data_code_pmc(system.file(
  "extdata", "PMID32171256-PMC7071725.xml", package = "rtransparency"
))
if (capabilities("libcurl")) rt_check_links(res$open_data_links)
#> # A tibble: 1 × 5
#>   link                  url                   status is_ok error
#>   <chr>                 <chr>                  <int> <lgl> <chr>
#> 1 https://osf.io/zrdx7/ https://osf.io/zrdx7/    200 TRUE  NA   
# }