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BeckyW edited this page Jun 3, 2026 · 1 revision

Welcome to the TreeScan-implementation wiki!

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

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