Tutorials

In this section, step by step tutorials will guide you through the different possibilities of GEMS.

• 1 - Getting Started
• • Hello World
  • Changing Parameters
  • Passing Parameters as Dictionaries
  • Comparing Scenarios
  • Getting the Raw Data
• 2 - Exploring Models
• • Exploring Individuals
  • Adjusting Individuals
  • Exploring Settings
  • Traversing
• 3 - Plotting
• • Plotting Results
  • Custom Plots
  • Plotting Maps
  • Custom Maps
  • Combining Plots
  • Saving Plots
  • Custom Plot Types
• 4 - Configuring Diseases
• • Static Mild Progression
  • Dynamic Mild Progression
  • Multiple Progressions
  • Age-based Progression Assignment
  • Complete Parameterization
• 5 - Running Batches
• • Repeating Simulations
  • process! Arguments
  • BatchData Objects
  • Custom BatchDataStyles
  • Running Scenarios
  • Attaching Interventions
  • Sweeping Parameter Spaces
  • Median Run
  • Multi-Group Median Runs
  • Reproducibility
• 6 - Creating Populations
• • Using Parameters
  • Using Dataframes
  • Using Inbuilt Models
  • Using Population Files
  • Using Settings-Files
  • Adjusting Populations
• 7 - Advanced Parameterization
• • Using Config Files
  • Using Contact Matrices
  • Custom Transmission Functions
  • Immunity & Waning
  • Custom Disease Progression
  • Custom Health Progression
  • Custom Progression Assignment
  • Custom Individual Extensions
  • Custom Start Conditions
  • Custom Contact Sampling
• 8 - Logging & Post-Processing
• • Internal Loggers
  • The PostProcessor
  • Custom Post-Processing
  • The ResultData object
  • Custom ResultDataStyles
  • Custom Loggers
• 9 - Intervention Strategies
• • Self-Isolation With Symptoms
  • Conditioned Measures (Isolation)
  • Household Isolation
  • Testing and Isolation
  • Delayed Measures (Testing)
  • Subpar Test (Poor Specificity)
  • Ghost Epidemic
  • Varying Test Sensitivity (or Specificity)
  • Limited Capacity (Testing)
  • Pool Testing
  • Recurrent Testing
  • Seroprevalence Testing
  • Multiple Test Types
  • Contact Reduction
  • Setting Closure
  • Custom Measures
  • Decaying Mandate Adherence
  • Adapting Behavior
• 10 - Calibration
• • Error Metrics
  • Define ResultData style
  • Calibrating a Single Parameter
  • Calibrating Setting Contact Rates
  • Multi-Parameter Calibration
  • Averaging Over Multiple Runs
  • Plotting the Training Curve
  • Using a Custom Loss Function