> For the complete documentation index, see [llms.txt](https://iddynamics.gitbook.io/flepimop/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://iddynamics.gitbook.io/flepimop/more/setting-up-the-model-and-post-processing/plotting-scripts.md).

# 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`; an ;
* a list of outputs to plot, `$OUTPUTS`, by default the script provides diagnostics for the following model output file ;

  ```r
  "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 ;


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