Add the Zenodo concept DOI to repository citation metadata

CITATION.cff

@@ -10,6 +10,10 @@ license: GPL-2.0-or-later
 title: 'bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in
   Traits'
 version: 0.2.2
+identifiers:
+- type: doi
+  value: 10.5281/zenodo.23268805
+  description: Zenodo concept DOI for all archived versions of bifrost.
 abstract: Methods for detecting, visualizing, and evaluating cladogenic shifts in
   multivariate trait data on phylogenies. Implements penalized-likelihood multivariate
   generalized least squares models and a greedy step-wise shift search for high-dimensional

README.md

@@ -5,6 +5,7 @@
 [![Codecov test coverage](https://codecov.io/gh/jakeberv/bifrost/graph/badge.svg)](https://app.codecov.io/gh/jakeberv/bifrost)
 [![CRAN status](https://www.r-pkg.org/badges/version/bifrost)](https://CRAN.R-project.org/package=bifrost)
 [![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/bifrost)](https://cran.r-project.org/package=bifrost)
+[![Zenodo concept DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23268805.svg)](https://doi.org/10.5281/zenodo.23268805)
 [![Package paper: Methods in Ecology and Evolution (in press)](https://img.shields.io/badge/package%20paper-MEE%20(in%20press)-005a70.svg)](#citation)
 [![Paper: Nature Ecology & Evolution](https://img.shields.io/badge/paper-Nature%20Ecology%20%26%20Evolution-000000.svg)](https://www.nature.com/articles/s41559-026-03110-5.epdf?sharing_token=PNALt0fkwK7zWng8AcHUw9RgN0jAjWel9jnR3ZoTv0MY7RbzUNNAnMQsco3ST9ehysSF4OiMNSc7ku-ywR1G5HC7BVOhY0inuNGDXiP16Z26oaZtwiblA-f61S2M-2llNRsRbegpuTeyhziEWzMipUgtyZKBEe3dsZlBVa67S4c%3D)
 [![bioRxiv preprint](https://img.shields.io/endpoint?url=https%3A%2F%2Fjakeberv.github.io%2Fbiorxiv-badge%2Fbadges%2F10.64898__2026.04.12.718036.json)](https://doi.org/10.64898/2026.04.12.718036)
@@ -187,6 +188,8 @@ If you use `bifrost`, please cite the package paper first listed below and the o
 citation("bifrost")
 ```
 
+Software releases are archived on Zenodo under the concept DOI [10.5281/zenodo.23268805](https://doi.org/10.5281/zenodo.23268805), which covers all archived versions of `bifrost`.
+
 ### Recommended citations
 
 1. `bifrost` methods / package paper\

cran-comments.md

@@ -23,7 +23,7 @@ timestamp check. Installation, examples and tests passed, with 2,980 passing
 test assertions and no test warnings or failures. The RNG chunk-invariance
 test now exercises two and three chunks using at most two worker processes.
 
-[CI](https://github.com/jakeberv/bifrost/pull/252/checks)
+[CI](https://github.com/jakeberv/bifrost/pull/254/checks)
 also checks macOS and Windows R release, and Ubuntu R release, devel and
 oldrel-1 (`--as-cran --run-donttest --no-manual`). A Windows temporary-file
 note was traced to the worker-cancellation test; its worker files now use a

tools/releases/0.2.2.md

@@ -59,7 +59,11 @@ for details. GitHub publication does not update CRAN automatically.
   complete the package and manual check with zero test warnings or failures.
 - [x] Preserve the two-versus-three-chunk RNG comparison using at most two real
   workers; also verify identical final caller RNG state.
-- [ ] Merge PR #252 through normal review and confirm its CI. Select the exact
+- [x] PR #252 merged as `f25e05cf`; all post-merge checks passed, including a
+  clean Windows check and exactly 100% coverage with zero uncovered rows.
+- [x] Rebuild and check the PR #254 source archive with the Zenodo README update,
+  including both manuals, in an isolated library.
+- [ ] Merge PR #254 through normal review and confirm its CI. Select the exact
   release commit and use the verified submission archive recorded below.
 - [ ] Retain the documented deferral of #231; this preparation does not fix it.
   Keep the initialization/convergence follow-up (#242) and RRphylo dependency
@@ -74,7 +78,30 @@ for details. GitHub publication does not update CRAN automatically.
 - [ ] Apply the publication-time documentation edits below through a PR.
   Update CRAN availability separately, only after CRAN actually publishes it.
 
-## Latest check: PR #252 Windows cancellation-test cleanup
+## Latest check: PR #254 Zenodo concept DOI update
+
+Source commit: `b3940d7c3cd2c8dec9392433358ea6823832b7bb`; checked on 2026-10-17 UTC.
+Archive SHA-256: `846b0c6b9c97c51f16f8937919c687959eb28a6fd7a2a2dd35a3249348dc1c70`.
+
+`R CMD check --as-cran --run-donttest`, including PDF and HTML manuals,
+returned **0 errors, 0 warnings, 1 note** (`unable to verify current time`).
+All **2,980 assertions passed**, with zero test warnings/failures and 138
+expected skips. The 101-page PDF also passed `qpdf --check`.
+
+Validation used a fresh isolated library with existing dependencies accessed
+read-only, two advertised cores, and one numerical thread per worker.
+Dependency DESCRIPTION hashes remained unchanged. Compared with the previous
+checked archive, only `README.md` and the generated packaging timestamp differ.
+The README contains the concept DOI badge/link; `CITATION.cff` is excluded from
+the CRAN archive as intended. No package code or tests changed.
+
+Evidence: `output/release-0.2.2-pr254-check/run-lnj56l9_/`, including the archive,
+`SHA256SUMS`, `final-summary.txt`, `bifrost.Rcheck/00check.log`, and the manual.
+Check the latest [PR #254 CI](https://github.com/jakeberv/bifrost/pull/254/checks)
+before merging. This archive supersedes the earlier archives recorded below;
+use its path and checksum for any later authorized submission.
+
+## Earlier check: PR #252 Windows cancellation-test cleanup
 
 Source commit: `87b6d31444424a90f823aebcbcbd291bbf80b5d6`; checked on 2026-10-17 UTC.
 Archive SHA-256: `4a817a3ab4e3f6c98efc01342ebaf8fb0b47b61287a05294d943c596a78a00dc`.