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PCM5 Generalized Mixed-Model Evidence Boundary

PCM5 extends the cichlid workflow into generalized mixed models and posterior phylogenetic quantities. It is the clearest example of a study family that is fully documented but not yet fully reproduced inside the repository.

flowchart LR
    A[Study sources and datasets] --> B[Governed evidence bundles]
    B --> C[Documented analytical map]
    C --> D[Posterior PGLMM boundary remains open]

What Is Source-Backed And Deployed

  • the lecture scripts and supplementary code references
  • the cichlid observation table, phylogeny, and saved workspace
  • governed bundle IDs for each checked-in evidence unit
  • the evidence map for posterior signal, ancestral values, count models, infection models, and repeated-measure random effects

What Is Not Yet A Repository-Owned Parity Claim

  • Poisson phylogenetic mixed-model posteriors
  • multinomial mixed-model posteriors
  • posterior ancestral-state ledgers
  • probability-scale posterior slope transforms
  • governed variance partitions matching the lecture's multi-random-effect models

What Readers Can Safely Conclude

  • the repository now documents the PCM5 lecture family at a much finer-grained evidence-ID level than one generic summary
  • the repository preserves the study inputs and analytical decomposition well enough for serious review
  • the remaining gap is not source intake or documentation quality; it is the posterior mixed-model reproduction boundary itself

Nearby Repository Support

The repository does expose narrower comparative surfaces such as binary-response comparative regression and reviewer-facing model-selection ledgers. Those are useful context, but they are not substitutes for the lecture's generalized mixed-model posterior workflow.

Reading Rule

Treat PCM5 as a documented study boundary with a strong source map. Do not read it as proof that the repository already owns a full PGLMM implementation.