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Evidence Book

This section explains the comparative study record behind the public phylogenetics runtime.

The repository currently exposes five study families and forty-three governed evidence bundles. Together they cover primate signal and regression studies, plus the cichlid mixed-model sequence. Some study families already carry stronger numerical parity records, while others still keep verdicts open because the scientific workflow depends on an external engine or on a lecture-specific boundary that has not been closed yet.

flowchart LR
    A[Source lecture] --> B[Public study guide]
    B --> C[Checked-in evidence dossier]
    C --> D[Freshness and integrity reports]
    C --> E[Study-specific evidence bundles]

Start Here

Treat those checked-in reports as the current source of truth when you need live repository status rather than the stable narrative on this page.

Evidence Program Snapshot

  • Five study families are published today: PCM1 through PCM5.
  • Every study family now has governed parity bundle IDs.
  • PCM1 and PCM2 currently provide the strongest end-to-end primate examples.
  • PCM3 keeps its lecture-specific interpretation boundaries explicit.
  • PCM4 and PCM5 remain scientifically useful, but they still rely on external posterior tooling for the largest open boundary.
  • Repository-wide freshness, integrity, and coverage-gap status lives in the checked-in review reports rather than in a manually maintained summary on this page.

Core Reading Order

  1. overview
  2. PCM1
  3. PCM2
  4. PCM3
  5. PCM4
  6. PCM5

That sequence mirrors the course progression. It starts with data and tree preparation, moves through comparative regression, and ends with the cichlid mixed-model studies where external posterior tooling remains the largest open boundary.

Study Atlas

Study Main question Evidence IDs Current repository state
Cichlid Bayesian Linear And Phylogenetic Mixed Models Where does the cichlid workflow move from standard regression into Bayesian mixed models with a phylogenetic effect? evidence-001 to evidence-007 (7 bundles) Governed parity bundles deployed; posterior workflow still external
Cichlid Phylogenetic Generalized Linear Mixed Models How do count models, binary-style models, repeated measures, and posterior signal estimates fit together in one study family? evidence-001 to evidence-009 (9 bundles) Governed parity bundles deployed; posterior workflow still external
Primate Continuous And Categorical Regression How should continuous predictors, categorical predictors, and interactions be interpreted together in comparative regression? evidence-001 to evidence-008 (8 bundles) Governed parity bundles deployed; lecture-specific verdicts remain open
Primate Longevity Signal How do primate traits and tree preparation become a usable signal and ancestral-state workflow? evidence-001 to evidence-009 (9 bundles) Governed parity bundles deployed; plotting boundary remains explicit
Primate PGLS And Signal How do baseline GLS, PGLS, transformed trees, and signal tests behave on the same primate dataset? evidence-001 to evidence-010 (10 bundles) Governed parity bundles deployed; one coverage boundary remains explicit

When To Use These Pages

  • Start with PCM1 if you want the full preparation path from raw primate traits and tree files to signal estimation and ancestral reconstruction.
  • Continue to PCM2 when you want to compare baseline GLS, PGLS, transformed trees, and signal testing on the same primate study.
  • Read PCM3 when the main question is how continuous predictors, categorical predictors, and interactions should be interpreted together.

  • Read PCM4 and PCM5 together when the main question is the cichlid mixed-model sequence, because they share the same dataset family and the same external posterior boundary.

  • Use the public study guides when you want the scientific story in plain language.

  • Use the checked-in evidence-book when you need provenance, registries, or bundle-level proof.
  • Use the index reports when you need freshness, integrity, or repository-wide gap tracking.

Reading Boundaries

  • These pages do not claim that every lecture has already been reproduced end to end inside the repository.
  • They do not hide external-tool dependencies just because nearby Python surfaces exist.
  • They do keep those limits visible, especially for PCM4 and PCM5.

Review Reports

The study record is useful because it keeps strong results visible without pretending that every workflow is fully reproduced inside the repository.