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rfair FAIR assessment

CRAN status R-CMD-check pkgdown Codecov test coverage Lifecycle: experimental License: GPL v3 DOI Archived on Software Heritage

Assess the FAIRness of research data objects and software, natively in R.

rfair is a native R implementation of the F-UJI (FAIRsFAIR Research Data Object Assessment) metrics. Given a persistent identifier or URL it resolves the object, harvests metadata from its landing page and from registries (DataCite, Crossref, GitHub), and scores it against the FAIRsFAIR metrics (v0.8 by default) for Findability, Accessibility, Interoperability, and Reusability.

rfair began as a fork of rfuji, an HTTP client for an external F-UJI server; unlike that client it performs the entire assessment in R — no Python, no server. It also scores research software against the FRSM (FAIR for Research Software) metrics, which operationalize the FAIR4RS Principles (Chue Hong et al. 2022).

It also goes beyond F-UJI with checks that automated FAIR tools usually miss (prompted by peer review of a COVID-19 FAIR-assessment study): whether a license actually permits reuse, whether data is controlled-access / sensitive, and whether identifiers follow best practices.

Installation

# From CRAN (when available)
install.packages("rfair")

# Development version from GitHub
# install.packages("remotes")
remotes::install_github("choxos/rfair")

Interactive app

No install required: a browser version (registry-only) is published at https://choxos.github.io/rfair/app/. Inside R, launch the bundled Shiny app:

launch_rfair()   # bslib Shiny app: scores, per-metric report, reuse/access panels

Quick start

library(rfair)

a <- assess_fair("https://doi.org/10.5281/zenodo.8347772")
a
#> <fair_assessment> https://doi.org/10.5281/zenodo.8347772
#>   resolved: https://zenodo.org/records/8347772
#>   metrics: v0.8 (17 metrics)
#>   FAIR      earned  percent  maturity
#>   F            7/7   100.0%         3
#>   A            7/7   100.0%         3
#>   I            4/6    66.7%         2
#>   R            5/6    83.3%         2
#>   FAIR       23/26    88.5%         2
# (illustrative; exact scores depend on the object's live metadata)

summary(a)            # F/A/I/R score table
as.data.frame(a)      # one row per metric
plot(a, type = "sunburst")   # concentric FAIR sunburst (also "category" / "metric")
as_fuji_json(a)       # F-UJI-compatible JSON
as_rdf(a)             # DQV + schema.org Rating (JSON-LD)

# Research software, scored against the FRSM metrics:
sw <- assess_fair("https://github.com/pangaea-data-publisher/fuji",
                  metric_version = "0.7_software")

fair4rs_principles()         # the FAIR4RS principles the software metrics map to
fair4rs_principles("R")      # filter to one foundational principle

Metric versions and F-UJI options

rfair bundles the current F-UJI website choices plus release-specific legacy metric files from upstream F-UJI:

rfair_metric_versions()
#> 0.8 0.5 0.5ssv2 0.5ss 0.5env 0.7_software ...

assess_fair(
  "https://doi.org/10.5281/zenodo.8347772",
  metric_version = "0.5ssv2",
  use_datacite = TRUE,
  metadata_service_endpoint = "https://example.org/oai",
  metadata_service_type = "oai_pmh"
)

Supported metadata service type labels include OAI-PMH, OGC CSW, SPARQL, DCAT, schema.org JSON-LD, DataCite, Crossref, Signposting, typed links, RO-Crate, CKAN, and a generic other metadata document option.

Beyond F-UJI

# A license can be present yet NOT open for reuse
license_reuse("https://creativecommons.org/licenses/by-nc-nd/4.0/")$is_open
#> [1] FALSE

# Controlled-access / sensitive data is not a FAIR failure
classify_access(access_level = "closedAccess",
                urls = "https://www.ncbi.nlm.nih.gov/gap/...")$controlled_access
#> [1] TRUE

# Identifier hygiene (layered / non-persistent PIDs)
identifier_hygiene("RRID:MGI:5577054")$issues

# Canonical FAIR principle definitions (go-fair.org / FAIR-nanopubs)
fair_principles("R")

These results are attached to every assessment (a$reuse, a$access, a$identifier_hygiene) and shown in the app.

Batch assessment and rtransparent

assess_fair_batch() scores a vector of identifiers and returns one tidy row per identifier. assess_data_code() bridges rtransparent: it takes the data and code identifiers rtransparent extracts from articles (its open_data_links and open_code_links columns; DOIs, repository URLs, and identifiers.org prefix:accession codes such as geo:GSE…) and scores each, using the FsF data metrics for data and the FRSM software metrics for code.

rt <- rtransparent::rt_data_code_pmc(xml)          # is_open_data, open_data_links, ...
scores <- assess_data_code(rt, id_col = "pmid")    # one row per (article, data/code link)

split_identifiers() parses the " ; "-joined link strings on their own.

HTTP API scaffold

rfair also ships a Plumber scaffold and OpenAPI contract for teams that want to expose the same assessment engine over HTTP:

api <- system.file("plumber", "rfair-api.R", package = "rfair")
pr <- plumber::pr(api)
pr$run(port = 8000)

The machine-readable API contract is installed at:

system.file("openapi", "rfair-openapi.yaml", package = "rfair")

How it works

id_parse() → resolve → harvest (DataCite JSON · landing-page JSON-LD/Dublin Core/
OpenGraph · signposting typed links · XML · RDF · GitHub) → merge → 17 metric
evaluators → F/A/I/R score → fair_assessment

Reference data (SPDX licenses, file formats, access rights, protocols, metadata standards, FAIR principles, reusabledata.org curations) is baked in from the F-UJI sources by the scripts in data-raw/.

Citation and metadata

The repository includes CITATION.cff and codemeta.json so software harvesters can find rfair’s authorship, license, version, dependencies, repository URL, and upstream F-UJI provenance. Each release is archived on Zenodo with a citable DOI; the concept DOI 10.5281/zenodo.20775127 always resolves to the latest version. Cite the version you used, or run citation("rfair").

Acknowledgements

rfair began as a fork of the rfuji F-UJI API client (Steffen Neumann) and reimplements the assessment engine natively in R. It is a native R port of F-UJI (© PANGAEA, MIT), itself based on the FAIRsFAIR metrics. The software metrics operationalize the FAIR Principles for Research Software (FAIR4RS): Chue Hong, N. P., Katz, D. S., Barker, M., Lamprecht, A.-L., Martinez, C., Psomopoulos, F. E., Harrow, J., Castro, L. J., Gruenpeter, M., Martinez, P. A., Honeyman, T., et al. (2022). FAIR Principles for Research Software (FAIR4RS Principles) (1.0). Research Data Alliance. https://doi.org/10.15497/RDA00068 (CC BY 4.0). License reusability uses the (Re)usable Data Project rubric; data FAIR principle definitions come from the FAIR-nanopubs vocabulary referenced by go-fair.org.

Use of AI

Parts of rfair were developed with the assistance of AI coding tools (Anthropic’s Claude, via Claude Code), including code drafting, documentation, and test scaffolding. All AI-assisted output was reviewed, tested, and verified by the author, who is solely responsible for the package and its correctness.

License

GPL-3. See https://www.gnu.org/licenses/gpl-3.0 for the full license text. rfair bundles reference data from external projects under their own (MIT, CC0-1.0, CC-BY-4.0) licenses; see LICENSE.note for the provenance and terms.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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