Diagnostic plotting scripts

We provide helper scripts to aid users in understanding model outputs and diagnosing simulations and iterations. These scripts may be set to run automatically after a model run, and are dependent on the model defined in the user's defined config file.

The script postprocess_snapshot.R requires the following command line inputs:

• a user-defined config, $CONFIG_PATH

• a run index, $FLEPI_RUN_INDEX

• a path to the model output results, $FS_RESULTS_PATH

• a path to the flepiMoP repository, $FLEPI_PATH; and

• a list of outputs to plot, $OUTPUTS, by default the script provides diagnostics for the following model output files

  "hosp, hpar, snpi, hnpi, llik"

Plots of hosp output files show confidence intervals of model runs, against the provided ground truth data for inference runs, for each metapopulation node. hnpi and snpi plots provide violin plots of parameter values for each slot.

Other scripts are included as more specific examples of post-processing, used for diagnostic tools. processing_diagnostics.R scripts provides a detailed diagnosis of inference model runs and fits.