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BeckyW edited this page Jun 3, 2026 · 1 revision

This page lists issues encountered while implementing the TreeScan approach. It includes both issues we are actively working to resolve and issues that have already been resolved, with links to the pages that address each resolved issue.

Current issues:

Resolved issues:

  • Fixed R script to download NSSP data so that pulls all available data for jurisdiction
  • Fixed R script to download NSSP data so that correct field is being pulled to define admit vs visit

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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