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PCM2: Primate PGLS And Signal

PCM2 is the deeper primate comparative study. It covers transformed trees, comparative model fitting, likelihood-ratio comparisons, baseline GLS, Pagel-lambda regression, and signal diagnostics on the same lecture family.

flowchart LR
    A[Baseline GLS] --> B[Tree transformation]
    B --> C[PGLS]
    C --> D[Signal diagnostics]

Why PCM2 Matters

PCM1 establishes the prepared study inputs. PCM2 asks whether more demanding comparative methods still behave coherently once phylogenetic correction and model comparison enter the picture.

Read PCM2 In Order

  1. Model comparisons and PGLS
  2. Signal diagnostics and open boundaries

Checked-In Study Dossier

The full checked-in record lives under evidence-book/studies/primate-pgls-and-signal/.

Inputs And Evidence Map

  • lecture source copies: primate_raw.xlsx, primate.RData, and primatetree.nex
  • governed derivatives: reference_primate.csv and reference_trimmed_primatetree.nwk
  • catalogs: dataset catalog and provenance guide
  • evidence bundles: evidence-001 through evidence-010

What To Take From PCM2

  • baseline GLS and phylogenetically corrected PGLS can be read as one comparative sequence
  • transformed trees and model comparisons belong in the same analytical story, not in separate islands
  • open boundaries can improve credibility when they remain visible

What Readers Should Watch Closely

  • whether the transformed-tree step changes only fit quality or also the comparative interpretation
  • whether model-comparison results are being read alongside the signal story instead of in isolation
  • whether the remaining open boundaries are made explicit rather than hidden under one generic "PGLS complete" claim

What PCM2 Does Not Prove

  • PCM2 does not close every comparative model in the repository.
  • It does not erase the remaining open boundaries named inside the study.
  • It does not substitute for release review or broader evidence-book coverage reports.