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PCM1: Primate Longevity Signal

PCM1 is the opening comparative case study in the evidence book. It follows the primate dataset from raw workbook and tree inputs through data repair, species alignment, phylogenetic signal, and ancestral reconstruction.

flowchart LR
    A[Raw workbook and tree] --> B[Prepared study inputs]
    B --> C[Signal analysis]
    C --> D[Ancestral reconstruction]

Why PCM1 Matters

Later studies only make sense if these earlier steps are already clear. PCM1 shows where the primate data came from, how the tree was trimmed, how the species alignment was made reviewable, and how the first comparative claims were bounded.

Read PCM1 In Order

  1. Data and tree preparation
  2. Signal and ancestral results

Checked-In Study Dossier

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

Inputs And Evidence Map

  • lecture source copies: primate_raw.xlsx, primate.RData, primate.csv, primatetree.nex, and trimmed_primatetree.nex
  • governed derivatives: reference_primate.csv and reference_trimmed_primatetree.nwk
  • catalogs: dataset catalog and provenance guide
  • evidence bundles: evidence-001 through evidence-009

What To Take From PCM1

  • preparation choices are visible before model fitting
  • signal and ancestral outputs stay tied to the same prepared study state
  • introductory evidence can be useful without pretending to close later regression or mixed-model questions

What PCM1 Does Not Prove

  • PCM1 does not close every comparative method in the repository.
  • It does not turn one primate teaching family into a general claim about all datasets.
  • It does not replace the broader freshness, integrity, or coverage reports.