TreeScan for the World Cup

🌳 TreeScan Implementation

A full pipeline for running TreeScan-based analyses using R and the TreeScan software.

This project provides a structured workflow to prepare data, run TreeScan, and process results using an R-based pipeline.

---

📦 Installation

1. Download this Repository

• Click the green Code button on GitHub
• Select Download ZIP
• Extract the ZIP file
• Locate the treescan_project subfolder
• Move treescan_project to your desired working directory

---

2. Install RStudio

Download and install RStudio: https://posit.co/download/rstudio-desktop/

---

3. Install TreeScan

Download TreeScan from: https://www.treescan.org/download_treescan.html

⚠️ Important setup details:

• You must create an account before downloading
• Choose version based on your environment:
  • Windows → if running locally
  • Linux → if running on a server
• Select the NON-graphical version
  • The standard (graphical) version may cause IT/access issues

---

4. Place TreeScan in Project Folder

After downloading:

Move the TreeScan files into the correct subfolder inside treescan_project:

Environment	Folder
Windows	TS_windows/
Linux	TS_linux/

---

🚀 Running the Pipeline

1. Open the Project in RStudio

• Launch RStudio
• In the bottom-right file explorer:
  • Navigate to: treescan_project/code/
  • Open: run_full_pipeline.R

---

2. Configure the Script

Before running, update the following:

Set Working Directory

Update line 4 to match your local path:

setwd("~/TreeScan-implementation/treescan_project")

Replace with wherever you saved treescan_project.

Set Execution Mode

Modify these variables depending on your setup:

server <- FALSE      # Set to TRUE if running on a server
first_time <- TRUE   # Set to FALSE after first run

---

3. Run the Pipeline

• Run the script in RStudio

The pipeline will:

• Execute TreeScan
• Process outputs
• Complete the full analysis workflow

---

⚠️ Notes

• Ensure the correct TreeScan version is placed in the matching folder (TS_windows or TS_linux)
• Using the non-graphical version is required
• Incorrect working directory paths will cause errors