This repository contains the Python code for my undergraduate thesis titled "Análisis de Convergencia en el Coalescente Seed-Bank: una aplicación del Método Monte Carlo" (Convergence Analysis in the Seed-Bank Coalescent: A Monte Carlo Application). The code simulates the SeedBank model and statistically verifies theoretical results on seedbank tree lengths.
Project Structure:
- CSV Folder: Stores CSV files used to generate the thesis's graphs. These files contain raw data for visualizations.
- Example Plots Folder: Demonstrates how the
plots.pyscript works. It includes plots generated from all CSV files in theCSV Folder. - pvalues.csv: The file contains the p-values shown in my thesis, for your reference, which were obtained with the seed 1602.
- Coalescent_SeedBank.py: Core script implementing simulations for the Kingman phase and Kingman phase with freezing.
- Plots.py: Generates plots from simulation results. It takes data and creates visualizations for exploration and analysis.
- Coalescent_Seed-Bank_Sigma.py: Simulates the complete coalescent tree, encompassing the entire model (from seed dispersal to coalescence). It builds upon
Coalescent_SeedBank.py. - Coalescent_Seed-Bank_Process.py: Simulates a single complete coalescent tree, saving all intermediate steps. This allows detailed tracking of the model's evolution for further analysis or debugging.
Required Libraries:
- pandas
- numpy
- scipy
- time
- tqdm
- matplotlib
- statsmodels
- glob