NOTE: You should put a GitHub API token in the environment variable `GITHUB_PAT` to fix rate limits. Acquire one at see https://github.com/settings/tokens.
Usage
register_render(
register = read.csv("register.csv", as.is = TRUE, comment.char = "#"),
filter_by = c("venues", "works", "persons", "organisations"),
outputs = c("html", "md", "json"),
config = c(system.file("extdata", "config.R", package = "codecheck")),
venues_file = "venues.csv",
persons_file = "persons.csv",
codecheck_repo_path = NULL,
from = 1,
to = nrow(register),
parallel = FALSE,
ncores = NULL,
verbose = FALSE,
check_zenodo_policy = TRUE,
check_researchequals_policy = TRUE,
prune_unreferenced_libs = TRUE,
prune_unavailable_metadata = FALSE
)Arguments
- register
A `data.frame` with all required information for the register's view
- filter_by
The filter or list o filters (if applicable)
- outputs
The output formats to create
- config
A list of configuration files to be sourced at the beginning of the rending process
- venues_file
Path to the venues.csv file containing venue names and labels
- persons_file
Path to a CSV with `orcid` and `wikidata` columns, the register's lookup of the people it knows Wikidata items for. Optional: a missing file is ignored.
- codecheck_repo_path
Optional path to the codecheck package repository for build metadata (default: NULL)
- from
The first register entry to check
- to
The last register entry to check
- parallel
Logical; if TRUE, renders certificates in parallel using multiple cores. Defaults to FALSE.
- ncores
Integer; number of CPU cores to use for parallel rendering. If NULL, automatically detects available cores minus 1. Defaults to NULL.
- verbose
Logical; if TRUE, shows detailed output including pandoc commands from rmarkdown::render(). Defaults to FALSE.
- check_zenodo_policy
Logical; if TRUE (the default), audits all Zenodo-hosted certificates against the CODECHECK community curation policy after rendering and reports the findings on the console. Never fails a render. Results are cached, so only a cold render pays for the extra requests; set to FALSE to skip them entirely.
- check_researchequals_policy
Logical; if TRUE (the default), audits all certificates published on ResearchEquals against the CODECHECK curation policy after rendering, including membership in the CODECHECK collection and, for AGILEGIS certificates, in the Reproducible AGILE collection, and reports the findings on the console. Never fails a render. Results are cached like the Zenodo ones; set to FALSE to skip them entirely.
- prune_unreferenced_libs
Logical; if TRUE (the default), removes directories under `docs/libs` that no rendered HTML file references any more (see [prune_libs()] and codecheckers/codecheck#89) once rendering finishes. Only actually runs after a complete, unfiltered render (`from`/`to` covering the whole register) with no certificate failures; otherwise the step is skipped with a message, since a partial render can leave HTML that still references a directory this would delete.
Logical; if TRUE, a certificate's OpenAlex ID or abstract that this render's live lookup conclusively confirms is no longer available (as opposed to a lookup that simply failed - network error, rate limit) is actually removed from the rendered output. Defaults to FALSE: such a confirmed absence is more often a query problem than a real removal upstream, so by default the previously rendered value is kept, and a lookup failure never removes anything regardless of this flag. See [resolve_external_field()].