CFA Round 18 Submission

[arik-shurygin]

Description

Submission does not include deaths, only incident hospitalizations.

• Team name: CFA
• Model Name: Scenarios
• Institution: CDC Center for Forecasting and Outbreak Analytics

[github-actions]

Run validation on files: 2024-04-28/inc hosp/2024-04-28-CFA-Scenarios0.parquet

Columns:

No errors or warnings found on the column names and numbers

Scenarios:

No errors or warnings found on scenario name and scenario id columns

Origin Date Column:

No errors or warnings found on the column 'origin_date'

Value and Type Columns:

No errors or warnings found on Value and Type columns

Target Columns:

❌ Error 602: The data frame does not contain projections for 'inc death' target(s).
🟡 Warning 602: No value found associated with the targets: inc death (optional), inc hosp (optional), cum death (optional), cum hosp (optional); output_type: quantile, mean.

Locations:

No errors or warnings found on Location

Sample:

No errors or warnings found on Sample

Quantiles:

No errors or warnings found on quantiles values and format

Age Group:

No errors or warnings found on Age_group

[LucieContamin]

Hi @arik-shurygin .

Thank you for your submission and welcome! I just wanted to verify that I understand correctly the sample ID numbering: there is no stochasticity, every models runs has a different run_grouping "grouped" by age_group, location, horizon, scenario_id, and, target. Is that correct?

Please let me know if any issues or questions,
Best, Lucie

[LucieContamin]

Also, thank you for the abstract, but would it be possible to re-format it to match the previous abstract format, please? You can find the information here: https://github.com/midas-network/covid19-scenario-modeling-hub/blob/master/data-processed/MyTeam-MyModel/2023-04-16-MyTeam-MyModel-Abstract.md

Please let me know if any issues or questions,
Best, Lucie

[tjhladish]

Hi @LucieContamin, would it be possible to set up a time to discuss how our replicates should be matched? I want to make sure that there's no confusion resulting from using terminology differently, etc.

[eahowerton]

Hi @tjhladish, we'd be happy to schedule a call to discuss. l just sent you an email with a few proposed times.

[github-actions]

No projection submission file in the standard SMH file format found in the Pull-Request. No validation was run.

[github-actions]

If the submission contains projection file(s) with quantile projection, a pdf containing visualization plots of the submission might be available and downloadable in the GitHub actions. Please click on 'details' on the right of the 'Validate submission' checks. The pdf is available in a ZIP file as an artifact of the GH Actions. For more information, please see here

[github-actions]

Run validation on files: 2024-04-28/inc hosp/2024-04-28-cfa_scenarios-model0.parquet, 2024-04-28/inc hosp/2024-04-28-CFA-Scenarios0.parquet

Columns:

No errors or warnings found on the column names and numbers

Scenarios:

No errors or warnings found on scenario name and scenario id columns

Origin Date Column:

No errors or warnings found on the column 'origin_date'

Value and Type Columns:

❌ Error 510: Each group combination should have one unique value. 5054400 unique groups have been identified with this issue. For example:
group: 2024-04-28, B-2024-03-01, 16, inc hosp, 45, 0-64, sample, 2;
group: 2024-04-28, B-2024-03-01, 16, inc hosp, 46, 0-64, sample, 2;
group: 2024-04-28, B-2024-03-01, 16, inc hosp, 47, 0-64, sample, 2;
etc.

Target Columns:

❌ Error 602: The data frame does not contain projections for 'inc death' target(s).
🟡 Warning 602: No value found associated with the targets: inc death (optional), inc hosp (optional), cum death (optional), cum hosp (optional); output_type: quantile, mean.

Locations:

No errors or warnings found on Location

Sample:

❌ Error 905: All the groups should contains the same number of trajectories per group. Please verify.

Quantiles:

No errors or warnings found on quantiles values and format

Age Group:

No errors or warnings found on Age_group

[github-actions]

Run validation on files: 2024-04-28/inc hosp/2024-04-28-CFA-Scenarios0.parquet

Columns:

No errors or warnings found on the column names and numbers

Scenarios:

No errors or warnings found on scenario name and scenario id columns

Origin Date Column:

No errors or warnings found on the column 'origin_date'

Value and Type Columns:

No errors or warnings found on Value and Type columns

Target Columns:

❌ Error 602: The data frame does not contain projections for 'inc death' target(s).
🟡 Warning 602: No value found associated with the targets: inc death (optional), inc hosp (optional), cum death (optional), cum hosp (optional); output_type: quantile, mean.

Locations:

No errors or warnings found on Location

Sample:

No errors or warnings found on Sample

Quantiles:

No errors or warnings found on quantiles values and format

Age Group:

No errors or warnings found on Age_group

[LucieContamin]

Hi @arik-shurygin ,

Thank you for the update. Can I ask what the difference with the first submission?
Also, just for information, I will update the abstract for R18 today and will be happy to update the information in this PR as soon as available.

Please feel free to let me know if any questions or issues,
Best,
Lucie

[LucieContamin]

Please find here the skeleton for the R18 abstract: https://github.com/midas-network/covid19-scenario-modeling-hub/blob/master/data-processed/MyTeam-MyModel/2024-04-28-MyTeam-MyModel-Abstract.md
Please feel free to let me know if any questions or issues,
Best,
Lucie

[tjhladish]

Hi @arik-shurygin ,

Thank you for the update. Can I ask what the difference with the first submission? Also, just for information, I will update the abstract for R18 today and will be happy to update the information in this PR as soon as available.

Please feel free to let me know if any questions or issues, Best, Lucie

Hi @LucieContamin, we noticed some problems with the timing of vaccine uptake during the fitting period, that in turn affected the parameter estimates and initial conditions used for the projection period. We have now re-run everything.

We're also including Hawaii now; it still is not a compelling projection, but it seems less clearly wrong than it was in our first results version.

Thanks,
Tom

[LucieContamin]

Thank you very much for the additional information.
I will keep the PR open for the updated abstract.

Please feel free to let me know if any questions or issues,
Best,
Lucie

[github-actions]

Run validation on files: 2024-04-28/inc hosp/2024-04-28-CFA-Scenarios0.parquet

Columns:

No errors or warnings found on the column names and numbers

Scenarios:

No errors or warnings found on scenario name and scenario id columns

Origin Date Column:

No errors or warnings found on the column 'origin_date'

Value and Type Columns:

No errors or warnings found on Value and Type columns

Target Columns:

❌ Error 602: The data frame does not contain projections for 'inc death' target(s).
🟡 Warning 602: No value found associated with the targets: inc death (optional), inc hosp (optional), cum death (optional), cum hosp (optional); output_type: quantile, mean.

Locations:

No errors or warnings found on Location

Sample:

No errors or warnings found on Sample

Quantiles:

No errors or warnings found on quantiles values and format

Age Group:

No errors or warnings found on Age_group

[LucieContamin]

Good morning,

Thank you for the abstract update. I see that it matches the R17 skeleton. I apologize if I was confusing but we updated the skeleton since last week, to a R18 specific. I updated the link in the PR but here it is: https://github.com/midas-network/covid19-scenario-modeling-hub/blob/master/data-processed/MyTeam-MyModel/2024-04-28-MyTeam-MyModel-Abstract.md Would it be possible to update to that format?

Please feel free to let me know if any questions or issues,
Best,
Lucie

[github-actions]

Run validation on files: 2024-04-28/inc hosp/2024-04-28-CFA-Scenarios0.parquet

Columns:

No errors or warnings found on the column names and numbers

Scenarios:

No errors or warnings found on scenario name and scenario id columns

Origin Date Column:

No errors or warnings found on the column 'origin_date'

Value and Type Columns:

No errors or warnings found on Value and Type columns

Target Columns:

❌ Error 602: The data frame does not contain projections for 'inc death' target(s).
🟡 Warning 602: No value found associated with the targets: inc death (optional), inc hosp (optional), cum death (optional), cum hosp (optional); output_type: quantile, mean.

Locations:

No errors or warnings found on Location

Sample:

No errors or warnings found on Sample

Quantiles:

No errors or warnings found on quantiles values and format

Age Group:

No errors or warnings found on Age_group

[LucieContamin]

Hi,

Thank you for the abstract update! I just have some minor questions and should be able to merge.
In the abstract:

• the section number/types of immune classes considered has been removed. However it's still present in the round 18. Your previous version contains the information:

# Number/type of immune classes considered 

Immune classes are stratified by infection history ($2^7$ possible histories, caused by 3 ancestral strains and 4 introduced during the projection) and vaccination history (0, 1, or 2+ doses of earlier vaccines, and seasonally vaccinated with the new vaccine during the projection).  Waning occurs across four bins; any kind of immunogenic event (infection or vaccination) moves people back to the least-waned bin. 

• Some sections titles are missing some information, for example Seasonality implementation instead of Seasonality implementation, e.g., whether seasonality varies by geography and which datasets are used to fit seasonal parameters

It's minor issue and I am happy to merge the PR as it is and update the abstract after by adding the missing information back and updating the title sections , if it's easier for you. However, if you prefer to add/edit the abstract directly, please let me know and I will keep the PR open.

Please feel free to let me know if any questions or issues,
Best,
Lucie

[tjhladish]

@LucieContamin please check if the abstract looks right now

[github-actions]

Run validation on files: 2024-04-28/inc hosp/2024-04-28-CFA-Scenarios0.parquet

Columns:

No errors or warnings found on the column names and numbers

Scenarios:

No errors or warnings found on scenario name and scenario id columns

Origin Date Column:

No errors or warnings found on the column 'origin_date'

Value and Type Columns:

No errors or warnings found on Value and Type columns

Target Columns:

❌ Error 602: The data frame does not contain projections for 'inc death' target(s).
🟡 Warning 602: No value found associated with the targets: inc death (optional), inc hosp (optional), cum death (optional), cum hosp (optional); output_type: quantile, mean.

Locations:

No errors or warnings found on Location

Sample:

No errors or warnings found on Sample

Quantiles:

No errors or warnings found on quantiles values and format

Age Group:

No errors or warnings found on Age_group

[LucieContamin]

Thank you very much for the update, it looks all good! I will merge the PR.

Thanks again, Lucie