pheagle_cosmo

Analysis codes for cosmological-parameter estimation in Python (MCMC via emcee) and MATLAB (GA, IMODE, PEOA). See the accompanying paper: https://arxiv.org/abs/2505.10299.

Contents (short)

• Python: mock generation, residuals, MCMC drivers, plotting utilities.
• MATLAB: evolutionary/heuristic optimization pipelines in ga_ap/, imode_ap/, peoa_ap/.
• Notebooks: analysis.ipynb (statistics) and reconstruction_demo.ipynb (plots).
• Results are saved to chains/.

Requirements

• Python 3.8+
  • Recommended: numpy, scipy, matplotlib, pandas, emcee, corner
  • Install example:

    python -m venv .venv
    source .venv/bin/activate
    pip install numpy scipy matplotlib pandas emcee corner

• MATLAB (for GA/IMODE/PEOA)
  • Global Optimization Toolbox
  • AstroPack (used by some MATLAB scripts)

Quickstart

1. Generate mock data

• Edit mocks/source/run_mock.py: set num_seeds (random seed ensures reproducibility).
• From repository root:

  cd mocks/source
  python run_mock.py
  python bin_sne_data.py   # if needed for SNe binning

• Outputs appear under mocks/.

2. Compute residuals (optional)

python make_residuals.py

3. Run MCMC (Python)

• MCMC drivers live in mcmc/. Example:

cd mcmc
python run_MCMC_CCRSD.py
python run_MCMC_CCRSDSNe.py

• Chains are stored in chains/.

4. Run EA / GA / IMODE / PEOA (MATLAB)

• Use bootstrap drivers boots_CC_RSD.m and boots_CC_RSD_SNe.m in:
  • ga_ap/, imode_ap/, peoa_ap/
• Edit the parallel loop indices (e.g., parfor k = 0:10) to select which mock realizations to process.
• Demo scripts included for single runs (with/without bootstrap).
• Results saved to chains/.

5. Post-processing & plots

• Statistical summaries: open analysis.ipynb.
• Reconstruction and corner plots: open reconstruction_demo.ipynb.
• Whisker plot for H0 / S8: make_H0S8_whisker.py.

Repository layout (key)

• mocks/ — mock inputs and outputs
• mcmc/ — MCMC drivers and settings
• ga_ap/, imode_ap/, peoa_ap/ — MATLAB pipelines
• chains/ — output results (by mock index)
• analysis.ipynb, reconstruction_demo.ipynb
• make_residuals.py, make_H0S8_whisker.py, utility modules

How to cite

If you use this code, please cite:

@article{Bernardo:2025flj,
    author = "Bernardo, Reginald Christian and Enriquez, Erika Antonette and Mendoza, Renier and Reyes, Reinabelle and Velasco, Arrianne Crystal",
    title = "{Nature-inspired optimization, the Philippine Eagle, and cosmological parameter estimation}",
    eprint = "2505.10299",
    archivePrefix = "arXiv",
    primaryClass = "astro-ph.CO",
    month = "5",
    year = "2025"
}