Part 2 - Refining the model

In this second part of the tutorial you will:

• Learn how to change a disease model by adding in an extra “infectious but asymptomatic” stage to the lurgy.

• Learn how to perform parameter sweeps to investigate how disease parameters change the population trajectories during a model run.

• Understand random error by running a parameter sweep with many repeats.

• Learn how to run metawards on a HPC cluster

• Learn how to examine a hypothesis and conduct a large model run on a cluster to gather evidence.

• Learn how to change the underlying geographic model data

• Refining the disease model
  • Understanding the disease file
  • Modifying the disease file
• Adjustable Variables
  • Choosing what to adjust
  • Output directories
• Analysing the output
  • Finding peaks
  • Plotting the output
  • Jupyter notebook
• Running on a cluster
  • Installing on a cluster
  • Setting up the job
  • Writing a job script
  • Running the HPC job
  • Processing the output
• Refining the model
  • Testing a hypothesis
  • Setting up the job
  • Running the job
  • Processing the output
  • Conclusion from experiment
• Model data
  • Alternative models