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System Maintenance Guide

Create fresh forecasts manually

For an end-to-end run:

  • Check your local version of the repository is up to date with git pull
  • Run bash/forecast.sh from the terminal
  • Check the output by looking plots saved in the most recent folder: evaluation/plots/yyyy-mm-dd
  • A properly formatted csv, ready to be submitted to the Reich forecast hub, will be saved in
    • submissions/submitted/yyyy-mm-dd-epiforecasts-ensemble1.csv

Note that the final submission file is a QRA ensemble with weighted quantiles by default. To check or change this:

  • Open submissions/finalise.R
  • Set global variables:
    • alter line 12 to filter for a different model.
  • If doing this:
    • Before running bin/forecast.sh: save the script and then run bin/forecast.sh
    • After running bin/forecast.sh: save and then source the script.

Runtime

Using the Epiforecasts azure VM (16 core), if bash/forecast.sh runs perfectly then the runtime is typically 1-2 hours

Debugging

  • If bin/forecast.sh errors: open as a script, run each command in sequence to check where it fails