3. Key Concepts

TODO: provide high-level explanations of the various components (e.g., simulation models, observation models, lookup tables and where they are stored, summary tables) and how they all fit together.

3.1. Scenario definitions

High-level overview of the TOML, how we allow for inheritance and overriding on a per-scenario basis.

3.2. Simulation models

3.3. Prior distributions

3.4. Observations

3.5. Observation models

3.6. Particle filter

TODO: explain how the particle filter combines all of the above to estimate the posterior distribution.

3.7. Time scales

3.8. Lookup (input) tables

3.9. Summary (output) tables

3.10. Summary monitors

3.11. Particle filter settings

3.12. Other simulation settings

3.13. Generating reproducible results

3.14. Plotting

3.15. HDF5