covid19-sir: [Fix] too long delay period of Hungary with Scenario.estimate_delay()
Summary
As discussed in #670, Scenario.estimate_delay() returns 53 days as delay period of hungary and this is too long. This causes change points detection failure in S-R trend analysis.
We may need to revise Scenario.estimate_delay() to get many data for “Period Length” calculation. We have only 11 records for Hungary as an example.
Codes
snl = cs.Scenario(country="Hungary", province=None)
snl.register(jhu_data, population_data, extras=[oxcgrt_data])
# 53, dataframe
delay, df = snl.estimate_delay()
# S-R trend analysis
_ = snl.trend()
Outputs
| Index | Confirmed | Stringency_index | Period Length |
|---|---|---|---|
| 0 | 48757 | 40.74 | NaN |
| 1 | 32 | 50 | 12 |
| 2 | 32 | 50 | 36 |
| 3 | 32 | 50 | 29 |
| 4 | 4183 | 54.63 | 17 |
| 5 | 94916 | 57.41 | 53 |
| 6 | 3990 | 61.11 | 31 |
| 7 | 3741 | 66.67 | 53 |
| 8 | 300 | 71.3 | 2 |
| 9 | 366279 | 72.22 | 5 |
| 10 | 2443 | 76.85 | 118 |
| 11 | 614612 | 79.63 | 19 |

Environment
- CovsirPhy version: 2.17.0-pi
- Python version: 3.9.2
- Installation: poetry
- System: WSL (Ubuntu)
About this issue
- Original URL
- State: closed
- Created 3 years ago
- Comments: 21 (11 by maintainers)
I think yes, because Q2 is stricter and more specific than
values < quantile(0.99).I like the idea with phase-specific delay period, and I agree we could either merge phases using this metric or RMSLE, whichever works better.
Sorry for the delayed test pull request, I will try to create it by tomorrow.