-
Notifications
You must be signed in to change notification settings - Fork 2
What a TreeScan signal means
A TreeScan signal indicates that the number of observed diagnoses in a particular diagnosis group and time window is higher than expected based on recent data patterns.
Signals therefore represent statistical anomalies, not confirmed outbreaks.
They serve as starting points for further investigation.
In practice, many signals arise for reasons unrelated to emerging health threats.
Common causes of signals include:
- changes in clinical coding practices
- data reporting delays
- local spikes at a single facility
- seasonal fluctuations
- random variation
Interpreting signals therefore requires contextual knowledge and additional data review.
When a signal is detected, analysts typically review additional information to determine whether the signal warrants further attention.
Common steps include:
- examining temporal graphs of diagnoses over time
- reviewing visit-level linelists
- checking whether the signal is concentrated at a single facility
- examining related diagnoses and chief complaints
- comparing the signal with historical patterns
These steps help determine whether the signal represents a plausible public health concern or a benign artifact.
TreeScan is designed to support surveillance workflows, not replace human judgment.
The method identifies unusual statistical patterns, but interpretation requires expertise in:
- epidemiology
- clinical practice
- healthcare data systems
- local public health context
TreeScan signals therefore function as alerts that guide further review, rather than definitive conclusions.
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.
- Click the green Code button on GitHub
- Select Download ZIP
- Extract the ZIP file
- Locate the
treescan_projectsubfolder - Move
treescan_projectto your desired working directory
Download and install RStudio:
https://posit.co/download/rstudio-desktop/
Download TreeScan from:
https://www.treescan.org/download_treescan.html
- 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
After downloading:
Move the TreeScan files into the correct subfolder inside treescan_project:
| Environment | Folder |
|---|---|
| Windows | TS_windows/ |
| Linux | TS_linux/ |
- Launch RStudio
- In the bottom-right file explorer:
- Navigate to:
treescan_project/code/ - Open:
run_full_pipeline.R
- Navigate to:
Before running, update the following:
Update line 4 to match your local path:
setwd("~/TreeScan-implementation/treescan_project")Replace with wherever you saved treescan_project.
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- Run the script in RStudio
The pipeline will:
- Execute TreeScan
- Process outputs
- Complete the full analysis workflow
- Ensure the correct TreeScan version is placed in the matching folder (
TS_windowsorTS_linux) - Using the non-graphical version is required
- Incorrect working directory paths will cause errors