r-pub-pipeline

name	r-pub-pipeline
description	Orchestrate the full R publication pipeline: CRAN submission for distribution, JOSS paper for DOI and peer review, optionally a JSS methods paper. Coordinates audits, drafting, and review cycles.

R Package Publication Pipeline

Orchestrate the full publication pipeline for R packages: CRAN submission → JOSS paper → optionally JSS methods paper. This skill coordinates the other skills (/cran-audit, /joss-audit, /joss-draft) into a coherent workflow.

Strategy

The recommended publication order for R packages:

1. CRAN — Distribution, discoverability, installation via install.packages()
2. JOSS — Quick DOI, peer-reviewed citation, Crossref/Google Scholar indexing
3. JSS (optional) — High-prestige methods paper, Web of Science indexed (IF ~5)

Each stage builds on the previous. CRAN gives the package legitimacy. JOSS gives it a citable DOI. JSS gives the methodology academic weight.

Workflow

Phase 1: Assess Current State

Start by understanding where the package stands:

Load user config (Read tool): Read .claude/pub-pipeline.local.md if it exists. Extract author metadata, r.domain, r.audience, r.competitors, r.targets (e.g., ["CRAN", "JOSS"]), and related_work from the YAML frontmatter. If related_work contains companion papers or preprints, note them, since they affect the JOSS paper (cite companion papers, reference preprint DOIs) and the overall publication strategy.

1. Read DESCRIPTION for package metadata (Read tool)
2. Check git log for development history (Bash tool)
3. Look for existing paper.md, CITATION.cff (Glob tool)
4. Check if already on CRAN — search https://cran.r-project.org/package={name} (WebFetch tool)
5. Check if already on JOSS — search joss.theoj.org (WebSearch tool)

Dependency chain (Bash tool): Parse Imports, Depends, and LinkingTo from DESCRIPTION. For each non-base/non-recommended package, verify it exists on CRAN:

Rscript -e 'ap <- available.packages(); cat("PKG_NAME" %in% rownames(ap))'

If any dependency is not on CRAN, this is a hard blocker — the package cannot pass R CMD check --as-cran. Present the submission order (publish dependencies first) and offer to switch to the dependency package. Also check r.dependency_chain in the user config for structured dependency status.

CI status (Bash/Glob tools): Check for .github/workflows/ directory (Glob tool). If present, check recent CI status:

gh run list --limit 3 --json conclusion,name,headBranch

Flag if CI is failing — passing CI is important for CRAN confidence and JOSS reviewer trust.

Classify the package into one of:

State	Next Step
Dependencies not on CRAN	Start with dependency package
Not on CRAN, no paper.md	Start with CRAN audit
On CRAN, no paper.md	Start with JOSS audit
On CRAN, has paper.md	Review paper, prepare JOSS submission
On CRAN, published in JOSS	Consider JSS (if substantive methodology)

Note: If the package is bioinformatics-focused (genomics, proteomics, etc.), consider Bioconductor instead of CRAN. Bioconductor has its own submission process and is the standard distribution channel for bioinformatics R packages.

Present the assessment to the user and confirm the plan before proceeding.

Phase 2: CRAN Readiness

Invoke /cran-audit (the cran-audit skill) to evaluate CRAN readiness.

If the package is not CRAN-ready:

1. Present the gap report
2. Offer to fix automatable issues
3. Guide manual fixes
4. Re-audit after fixes
5. Walk through submission workflow when ready

If the package is already on CRAN, skip to Phase 3.

Key CRAN submission steps (when ready):

1. usethis::use_version("minor") — bump version
2. devtools::check(args = "--as-cran") — final check
3. Test on other platforms:
   • devtools::check_win_devel() — Windows (win-builder)
   • rhub::rhub_check(): multiple platforms via R-hub v2 (one-time setup: rhub::rhub_setup(); use rhub::rc_submit() for non-GitHub repos). The old rhub::check_for_cran() is defunct since rhub v2.
4. devtools::submit_cran() — submit
5. Confirm via email link
6. After acceptance: usethis::use_github_release(), then usethis::use_dev_version()

If CRAN rejects the submission:

1. Read the reviewer's email carefully — they identify specific issues
2. Fix all identified issues (do not partially fix)
3. Re-run devtools::check(args = "--as-cran") to verify
4. Resubmit via devtools::submit_cran() — CRAN allows resubmission
5. In cran-comments.md, note what was fixed since the previous submission
6. Do not resubmit more than once per week unless requested by CRAN

Phase 3: JOSS Readiness

Invoke /joss-audit (the joss-audit skill) to evaluate JOSS readiness.

Key prerequisites that are often missing:

• Development history: Need 6+ months of public git history
• Contributing guidelines: CONTRIBUTING.md or section in README
• paper.md: The JOSS paper itself

If paper.md doesn't exist, proceed to Phase 4.

Phase 4: Draft JOSS Paper

Invoke /joss-draft (the joss-draft skill) to draft paper.md and paper.bib.

After drafting:

1. Present the draft to the user for review
2. Iterate on feedback
3. Optionally run the pub-pipeline:joss-reviewer agent (via /joss-audit) for critical review against the JOSS checklist
4. Commit the paper to the repository

Phase 5: JOSS Submission

Walk the user through JOSS submission:

1. Pre-submission checklist:

   • Package on CRAN (or at minimum, installable from GitHub)
   • paper.md and paper.bib committed to repository
   • All JOSS reviewer checklist items pass (/joss-audit)
   • ORCID for all authors

2. Submit:

   • Go to https://joss.theoj.org/papers/new
   • Fill in repository URL and other fields
   • Wait for pre-review issue

3. During review (2-6 weeks):

   • Respond to reviewer feedback promptly (target 2 weeks)
   • Make requested changes to code and paper
   • Re-run /joss-audit after changes

4. Post-acceptance:

   • Create tagged release (e.g., v1.0.0)
   • Deposit on Zenodo:
     1. Go to https://zenodo.org and log in with GitHub
     2. Enable the Zenodo-GitHub integration for this repository (Settings → GitHub)
     3. Create a GitHub release (this triggers automatic Zenodo archiving)
     4. Copy the Zenodo DOI from the automatically created deposit
   • Update review issue with version number and Zenodo DOI
   • JOSS assigns paper DOI via Crossref

Phase 6: JSS Consideration (Optional)

Evaluate whether a JSS (Journal of Statistical Software) paper is warranted:

JSS is appropriate when:

• The package implements novel statistical methodology
• There's substantive mathematical content to present (proofs, derivations)
• The paper would be 20-50 pages of methods + software description
• The target audience is academic statisticians

JSS is NOT appropriate when:

• The package is primarily a software tool (JOSS covers this)
• The mathematics is textbook material
• The paper would essentially repeat the JOSS paper at greater length

If JSS is appropriate, note that:

• JSS uses rticles::jss_article RMarkdown format
• JSS papers are 20-50 pages and include mathematical exposition
• JSS is indexed in Web of Science (Impact Factor ~5)
• Review takes 6-18 months
• The papermill:writer agent can help draft a full JSS paper (long-form academic writing)

Decision Helpers

Is My Package Publishable?

Criterion	Minimum for CRAN	Minimum for JOSS
License	OSI-approved	OSI-approved
Tests	Pass R CMD check	Automated test suite
Docs	Man pages for exports	README + examples + API docs
History	Any	6+ months public
Users	Not required	Evidence of use encouraged
Paper	Not required	750-1750 word paper.md

Timeline Expectations

Stage	Duration
CRAN prep + audit	1-3 days
CRAN review	1-7 days (usually 1-2)
JOSS prep + paper	1-2 days
JOSS review	2-8 weeks
JSS prep + paper	2-4 weeks
JSS review	6-18 months

Reference Files

• ${CLAUDE_PLUGIN_ROOT}/docs/cran-reference.md — CRAN Repository Policy, submission workflow, common rejections
• ${CLAUDE_PLUGIN_ROOT}/docs/joss-reference.md — JOSS requirements, reviewer checklist, paper format
• ${CLAUDE_PLUGIN_ROOT}/docs/joss-exemplars.md — Real JOSS R package papers with analysis

Important Notes

• Never submit to JOSS before the package is installable (ideally on CRAN).
• CRAN and JOSS are complementary: CRAN for distribution, JOSS for citation.
• Each publication stage builds credibility for the next.
• The user controls the pace — present options, don't push.