A generalized numerical model for clonal growth in scleractinian coral colonies

Coral reefs, vital ecosystems supporting diverse marine life, are primarily shaped by the clonal expansion of coral colonies. Although the principles of coral clonal growth, involving polyp division for spatial extension, are well-understood, numerical modeling efforts are notably scarce in the literature. In this article, we present a parsimonious numerical model based on the cloning of polyps, utilizing five key parameters to simulate a range of coral shapes. The model is agent-based, where each polyp represents an individual. The colony's surface expansion is dictated by the growth mode parameter (s), guiding the preferred growth direction. Varying s facilitates the emulation of diverse coral shapes, including massive, branching, cauliflower, columnar, and tabular colonies. Additionally, we introduce a novel approach for self-regulatory branching, inspired by the intricate mesh-like canal system and internode regularity observed in Acropora species. 
Through a comprehensive sens..., , , # A generalized numerical model for clonal growth in scleractinian coral colonies

### Authors: Eva Llabrés, Eleonora Re, Naira Pluma, Tomàs Sintes, and Carlos M. Duarte

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## Contents:

### 1. Code

* **File:** `code.zip`
* **Description:** This archive contains Python notebooks that can be run to reproduce the figures included in the article.
* **Languages:** Python, with dependencies on C++ and MATLAB libraries
*
* **Instructions:**
* Extract the contents of `code.zip`.
* Follow the instructions to set up the environment, dependencies and libraries.
* Run the Jupyter notebooks  to reproduce the results.

### 2. Data

* **File:** `data_measurements.txt`
* **Description:** This file contains the magnitudes measured in coral colonies (such as volume, surface, number of polyps, etc.) for every colony type. These measurements are extracted from `LLABRES_objects_ESM.zip`. Units included in the .txt file.
* **Format:**
* Columns:
* Volume
* Surface Area
* N...