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R

rgm

INFRA · APIS
Velocity0.0

Advanced Inference with Random Graphical Models

github.com/franciscorichter/rgm ↗

A microbiome network model that got itself un-archived by deleting the dependency that killed it.

microbiomegraphical-modelsbayesian-inferencecran-maintenancer-package
◆Current state
rgm implements the random graphical model for microbiome interactions across related environments, published in JABES in 2026. The package was archived from CRAN in February 2026 because of its dependency on huge; the recovery release drops that dependency entirely, which cost it the graphical-lasso warm start that used to seed the initial graph — the default is now an empty graph, with warm starts left to the user. A post-processing function returning ggplot diagnostics arrived in the same release.
◆Where it's heading
Three tags shipped inside two hours on one day, and the notes are candid about why: 1.1.0 held the actual work but was never released, 1.2.0 restated it under a higher version to signal the size of the change, and 1.2.1 answered CRAN pre-test feedback. Beyond the archival recovery, the visible work is housekeeping that had accumulated — a shadowed rmvnorm() definition, roxygen import tags that were silently emitting nothing, leftover C++ template scaffolding, and build artifacts under version control. The diagnostics function is the only genuinely new user-facing capability in the window.
◆Prediction
The immediate task was restoring availability, and that is done; the open question the entries raise is whether losing the graphical-lasso warm start affects convergence in practice, which the new diagnostic plots are positioned to answer.

◆Recent moves

  1. 3mo ago

    Journal DOI replaces the preprint; promotional wording removed

    CRAN pre-test follow-up: the description now cites the published JABES article rather than the arXiv preprint, promotional language is struck, and the citation year is corrected throughout. Metadata only.

    View source ↗
  2. 3mo ago

    Back on CRAN after dropping the dependency that caused archival

    The release that actually shipped, restoring availability three months after archival by removing the huge dependency. The trade is visible in the default: initial graphs are now empty rather than seeded by a graphical-lasso warm start, and users wanting one must supply it. A post-processing function returning six diagnostic plots is the release's one addition.

    View source ↗
  3. 3mo ago

    Unreleased twin of the CRAN recovery release

    Carries the same changes as the version published 42 minutes later, which the later notes confirm explicitly — this tag was never released, and the version was bumped to make the scope of the change legible. Its notes are the fuller of the two, enumerating all six diagnostic plots.

    View source ↗
  4. 2y ago

    First release: simulation, estimation and post-processing

    The founding release, listing three function groups in a single line each. It establishes the package's shape — simulate, estimate, post-process — but carries no description of the model itself, so the capability has to be read from the published article rather than the changelog.

    View source ↗