PCM5: Cichlid Phylogenetic Generalized Linear Mixed Models¶

PCM5 is the most demanding lecture family in the current evidence book. It combines posterior phylogenetic signal, ancestral-state extraction, count models, binomial-style models, and repeated measures.

flowchart LR
    A[Count models] --> B[Binary-style models]
    B --> C[Repeated measures]
    C --> D[Posterior signal and ancestral summaries]

Why PCM5 Matters¶

PCM5 needs careful documentation because it is easy to blur together distinct model families and distinct scientific questions.

Read PCM5 In Order¶

Generalized mixed-model evidence boundary

Checked-In Study Dossier¶

The full checked-in record lives under evidence-book/studies/cichlid-phylogenetic-generalized-linear-mixed-models/.

Inputs And Evidence Map¶

lecture source copies: cichlid.csv, cichlidtree.nex, fishdata.RData, PCM5_PGLMM.R, and PCM5_extra_code.R
catalogs: dataset catalog and provenance guide
evidence bundles: evidence-001 through evidence-009

What To Take From PCM5¶

count, binary-style, ancestral, and repeated-measure questions need to stay separate
the repository already preserves that separation in the study breakdown
nearby binary comparative utilities are context, not a substitute for the lecture's full posterior mixed-model workflow

What Not To Overread¶

PCM5 does not claim a repository-owned replacement for the lecture's full posterior PGLMM workflow
it does not merge distinct model families into one oversimplified summary
it does not treat nearby binary regression support as proof of full mixed model reproduction