CHANGES:

1. `thin_samples['init_state']` --> `thin_samples['initial_state']`
2. `thin_samples['events']` --> `thin_samples['seir']`
3. add time dimension to next generation matrix
4. update downstream scripts to changes.

CHANGES:

1. Replaced `read_phe_cases` with `CasesData`
2. Column-name fix in `case_exceedance`
3. Fix column heading in `summarize.infec_incidence`
4. Add Rt_exceed to `summarize.rt`
5. Add layer option to `summary_geopackage`
6. Update `ruffus_pipeline.py` to reflect above changes
7. Update `template_config.yaml` to reflect above changes