riskintroapp

Shiny application for estimating the risk of an animal disease being introduced into a geographical area. The app can be used solely with user data but also provides datasets derived from World Animal Health Information System (WAHIS).

Installation

You can install riskintroapp from GitLab using the remotes package:

# Install pak if you don't have it
install.packages("pak")
pak::pak("git::https://gitlab.cirad.fr/astre/riskintro-app/riskintroapp.git")

# Accept updates to 
#  + riskintrodata    
#  + riskintroanalysis
#  + riskintroapp
#  + ideally any other dependencies

Running the Application

Launch the Shiny application with:

riskintroapp::run_riskintro()

Workflow

The typical workflow in riskintroapp follows these steps:

1. Import epidemiological units: Load geospatial data (shapefile, GeoPackage, or GeoJSON) defining the administrative boundaries or regions you want to analyze

2. Configure emission risk factors: Either import WAHIS outbreak data for your disease of interest or manually define emission risk factors for source countries/regions

3. Calculate introduction risks: Analyze risk from multiple pathways:

   • Border risk: Risk from shared land borders with neighboring regions
   • Entry point risk: Risk from ports, airports, and border crossings
   • Animal mobility risk: Risk from livestock movements between regions
   • Road access risk: Risk based on transportation infrastructure connectivity
   • Additional risks: Additional user-defined risk factors

4. Rescale risk scores: Transform calculated risks to a common 0-100 scale using linear, quadratic, exponential, or sigmoid methods

5. Aggregate results: Combine risks from different pathways using mean, maximum, minimum, or median aggregation

6. Visualize and export: View results on interactive maps and tables

Saving your work

Use the Workspace tab to save and restore your complete analysis session:

• Save workspace: Exports all imported data, calculated risks, scaling parameters, and settings to a single file
• Load workspace: Restores a previously saved session to continue your analysis
• Session persistence: All data, configurations, and results are preserved between sessions

This allows you to: - Share complete analyses with colleagues - Return to previous work without re-importing data - Maintain reproducible analysis workflows - Compare different risk scenarios

Related Packages

riskintroapp depends on two companion packages that provide the underlying analysis methods and data management tools:

riskintroanalysis

Analysis methods for calculating animal disease introduction risk scores.

• Documentation: https://astre.gitlab.cirad.fr/riskintroanalysis
• Source Code: https://gitlab.cirad.fr/astre/riskintro-app/riskintroanalysis
• Bug Reports: https://gitlab.cirad.fr/astre/riskintro-app/riskintroanalysis/-/issues

riskintrodata

Data management tools for importing and validating risk analysis datasets.

• Documentation: https://astre.gitlab.cirad.fr/riskintrodata
• Source Code: https://gitlab.cirad.fr/astre/riskintro-app/riskintrodata
• Bug Reports: https://gitlab.cirad.fr/astre/riskintro-app/riskintrodata/-/issues

License

MIT + file LICENSE