155 lines
4.6 KiB
Markdown
155 lines
4.6 KiB
Markdown
# renunney
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Working repository for replication and reanalysis of Leonard Nunney's 2003
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cost-of-substitution simulations.
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## Biological Question
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Nunney's paper asks how rapidly an adapting population can track a moving
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environment before extinction becomes likely. In this model:
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- the selective optimum moves steadily through time,
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- adaptation requires repeated allelic substitutions across one or more loci,
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- population growth is density-dependent,
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- offspring survival falls as genotypes lag behind the moving optimum,
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- and "cost of substitution" is summarized by the smallest environmental-change
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interval `T` that still allows persistence.
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Smaller `T` means faster environmental change and a harder adaptive problem.
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## Two Approaches
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This project treats the problem in two separate ways.
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Track 1: Nunney-faithful replication
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- reconstruct the published simulation and threshold heuristic as closely as
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possible,
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- preserve historically relevant assumptions even when they are inefficient or
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awkward,
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- and use that result as the baseline for replication and criticism.
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Track 2: modern replacement
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- build a cleaner and faster simulator around the same biological question,
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- define threshold explicitly rather than through Nunney's heuristic,
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- and use a more performant implementation path, likely including Rust.
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The current repo is centered on Track 1, with orchestration intended to support
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both tracks later.
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## Nunney's Approach
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The paper-level model combines four pieces:
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- constant environmental change,
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- genotype survival `w_i` as a function of distance from the moving optimum,
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- density-dependent female fecundity `f`,
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- and Mendelian transmission with mutation.
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The published threshold procedure is heuristic rather than inferential: Nunney
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searches for the smallest `T` with no extinctions in 20 runs, then checks
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nearby larger values. That historical rule is preserved in Track 1 because it
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is part of the claimed result structure.
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## This Repo's Approach
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`renunney` turns that work into a clean, testable stack:
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- local Track 1 simulation kernel,
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- local threshold/search layer,
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- local analysis, reporting, extinction-dataset, and fitting layers,
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- local orchestration CLI and SQLite job registry,
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- local paper-scale Figure 1 configs,
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- and a Makefile for common operational tasks.
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The repo was bootstrapped from earlier work in
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[`../collaborations/to_ptbc/evc/cost_of_substitution`](/mnt/CIFS/pengolodh/Docs/Projects/collaborations/to_ptbc/evc/cost_of_substitution),
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which remains useful as provenance and historical context, but the Track 1
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runtime now lives in `renunney`.
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## Key Docs
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- [docs/MIGRATION.md](/mnt/CIFS/pengolodh/Docs/Projects/renunney/docs/MIGRATION.md)
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- [docs/WORKFLOW.md](/mnt/CIFS/pengolodh/Docs/Projects/renunney/docs/WORKFLOW.md)
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- [docs/NUNNEY_ANALYSIS.md](/mnt/CIFS/pengolodh/Docs/Projects/renunney/docs/NUNNEY_ANALYSIS.md)
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- [docs/RESULTS_IN_HAND.md](/mnt/CIFS/pengolodh/Docs/Projects/collaborations/to_ptbc/evc/cost_of_substitution/renunney/docs/RESULTS_IN_HAND.md)
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- [docs/TRACK2_RUST.md](/mnt/CIFS/pengolodh/Docs/Projects/renunney/docs/TRACK2_RUST.md)
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## Layout
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- `docs/`
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project, migration, and paper-analysis notes
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- `config/`
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configuration templates and paper-scale treatment configs
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- `runs/state/`
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SQLite registries and persistent orchestration state
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- `runs/results/`
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result artifacts collected by orchestration
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- `runs/scratch/`
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local worker scratch and cache files
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- `src/renunney/`
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in-repo Python package
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- `scripts/`
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local CLI entrypoints
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- `tests/`
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local verification
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## Start
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Initialize the local run directories and SQLite registry:
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```bash
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make init
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```
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Run one local Track 1 simulation:
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```bash
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make track1-sim-smoke
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```
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Verify the Track 2 Rust workspace:
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```bash
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make rust-check
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make rust-test
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make rust-smoke
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```
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Compare Python Track 1 and the current Rust smoke kernel over multiple seeds:
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```bash
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make compare-track1-rust-smoke
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```
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Submit a paper-scale Figure 1 treatment:
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```bash
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make submit-figure1-m10
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```
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Run one worker loop locally:
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```bash
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make run-loop
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```
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Collate completed Figure 1 jobs:
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```bash
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make collate-figure1
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```
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## Status
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The Track 1 runtime and orchestration stack are now local to `renunney`.
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Track 2 has also started: the repo now includes a Rust workspace and an
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usable `track2-core` crate for threshold-centered work plus a minimal
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Nunney-style smoke kernel. The current next major steps are:
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- hardening multi-host orchestration for Track 1 replication,
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- organizing publication-quality replication outputs,
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- and turning the current Rust smoke framework into a stable Track 2 execution
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path with better statistical parity checks and tighter mechanics.
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