Ant Tracking

⚠️ Warning: Work in Progress

This is a re-organized version of PhD-exp1-data-analysis. Please note that this repository is still being updated. Older versions or missing files can be found in the original repository.

📍 Overview

Code used for Adriano Wanderlingh's Lasius niger Group Size Effects Experiment. 🐜 🦠

Testing Social Immunity role in disease hindering dynamics in societies, using ant colonies interaction networks and behaviour | experimental epidemiology.

R and C++ scripts for:

• Tracking Data Post-processing
• Geometrical capsules assignment
• Interactions detection
• Machine Learning Behavioural Classification
• Personal immunity investment and pathogen load quantification
• RTqPCR data pre-processing pipeline with MNAR data simulations
• extra related material

The repository is organized into two main folders: Scripts and Data. The Scripts folder contains R and C++ code for data processing, analysis, and visualization. The Data folder contains raw and processed data files.

Table of Contents

• Folder Structure
• Scripts
  • PhD-Ant_Colonies_Tracking_Analysis
    • Automated_Behavioural_Inference
    • molecular_bio_analysis
  • code_Social_Network_Plasticity_Exp_2018_AW
• Data
  • PhD-Ant_Colonies_Tracking_Analysis
    • Automated_Behavioural_Inference
    • molecular_bio_analysis

📂 Folder Structure

.
├── Scripts
│   ├── PhD-Ant_Colonies_Tracking_Analysis
│   │   ├── Automated_Behavioural_Inference
│   │   └── molecular_bio_analysis
│   └── code_Social_Network_Plasticity_Exp_2018_AW
│       ├── 1_data_post_processing
│       │   └── source
│       └── 2_statistics_and_plotting
│           └── source
└── Data
    └── PhD-Ant_Colonies_Tracking_Analysis
        ├── Automated_Behavioural_Inference
        └── molecular_bio_analysis

Scripts

PhD-Ant_Colonies_Tracking_Analysis

Data_preparation_after_postprocessing

For more information, read the folder README and the pre-processing_Adriano_June2022 guide.

Automated_Behavioural_Inference

For more information, read the folder README

molecular_bio_analysis

This folder contains scripts for molecular biology analysis, including qPCR and RT-qPCR analysis.

code_Social_Network_Plasticity_Exp_2018_AW

This folder contains scripts for data post-processing and statistical analysis of ant behavioural interactions, adapted from Stroeymeyt et al., 2018.

Data

PhD-Ant_Colonies_Tracking_Analysis

Automated_Behavioural_Inference

• Mean_ant_length_per_TrackingSystem.txt: [Information needed]

molecular_bio_analysis

• Adriano_RTqPCR_immune_genes_MASTER_REPORT.csv: [Information needed]
• Adriano_qPCR_pathogen_load_MASTER_REPORT.csv: [Information needed]

👏 Acknowledgments

• Code written by Adriano Wanderlingh, Nathalie Stroeymeyt and Tom Richardson with contributions by Enrico Gavagnign. Ant Epidemiology Stroeymeyt Lab, University of Bristol, UK

This file was generated by extracting information on the repo with README-AI and using find . d > dirs.txt to get the folder structure, then feeding both to GPT-4, which was prompted to write a README.md file.