Release NCHS Mortality

[krivard]

• Link to issue
• Link to PR
• Proposed release version: 1.11

This is a new indicator that's completed its first phase of development and is ready to consider for public release. This indicator tracks the number of covid, pneumonia, and all deaths, as well as the percentage of expected deaths, as published by the NCHS. Signal is per week, but the estimate is updated daily.

Edit: we will not pursue map release at this time

• Statistical review (usually correlations)

• Signal / source name review (usually Roni)

• Add to Delphi Automation

• API support for weekly data

• Visual review

• Signal description pop-up text drafting and review

• Map release notes

• API documentation and/or changelog

• API mailing list notification

[benjaminysmith]

Thanks Katie -- would you like me to shepherd the sub-tasks? Do you have an example of the process I can copy?

[krivard]

I would! Some examples are in the links, but this is still a prototype of the process we'd like to build, so not everything has something to go off of.

The tasks are roughly in order -- eg if the statistical review doesn't go off, we don't want to move forward until that's been fixed.

Jingjing should handle the statistical review. Anyone can handle putting together the signal and source naming recommendations (just send Roni a txt when he should look at the approvals doc and when it's needed by -- 1.11 isn't on the calendar yet so several days allowance is fine). Adding to automation will coordinate with Brian. Visual review, signal description pop-up text, and map release notes will coordinate with Chris. API documentation and mailing list notification will coordinate with Kari, Jingjing, and Alex.

[benjaminysmith]

Fabulous thanks!

@jingjtang looks like you are up for the first task. Ping me if you need help and I can escalate.

[jingjtang]

@benjaminysmith Simple comparison between usa-facts deaths_incidence_num vs nchs wip_covid_deaths_num. They are consistent each other in general but difference exists. The extent of difference varies among states.
covid_deaths_num.pdf

As for the correlation APP, it seems there is not a weekly response to use. A simple geo-wise spearman correlation analysis is shown below. Note that there is no lag considered(according to the figures in the pdf). The drop in the last few weeks is reasonable, since deaths usually have significant delay in reports. According to NCHS, this delay can range from 1 week to 8 weeks or more, depending on the jurisdiction and cause of death.

[jingjtang]

@krivard As for the signal names, the current ones are:

• covid_deaths_num
• covid_deaths_prop
• total_deaths_num
• total_deaths_prop
• influenza_deaths_num
• influenza_deaths_prop
• pneumonia_deaths_num
• pneumonia_deaths_prop
• pneumonia_and_covid_deaths_num
• pneumonia_and_covid_deaths_prop
• pneumonia_influenza_or_covid_19_deaths_num
• pneumonia_influenza_or_covid_19_deaths_prop
• percent_of_expected_deaths

as described here

what kind of txt do you need?

[jingjtang]

Though there is no geo aggregation needed, but we need population info for prop signals, so still need the geo refactor #382 . However, state names (e.g. Alabama, Alaska) are used in the raw dataset which has not been supported by our geo utils. Need @dshemetov 's confirmation. (Edited: new PR merged yesterday, now state names are supported in geo utils)

[jingjtang]

Contacted @korlaxxalrok already for the automation. Will work with him once he starts on this.
As for the automation, some important points for this pipeline

• A token is needed. Either use mine or create another one for Delphi.
• Code related to export_start_date should be changed according to the final strategy
• Data versioning staffs (run and store diffs daily but export to API weekly), might need @eujing 's help.

[RoniRos]

@jingjtang :

1. Is there significance to the use of 'and' vs. 'or' in the signal names above? Does pneumonia_and_covid_deaths_num count deaths that have been classified as due to BOTH pneumonia AND Covid, or those that have been classified as due to Influenza + those classified as due to Covid?

2. In this description, it's important to clearly mention whether the classification is based only on the primary ICD code (primary cause of death), or on 'any code'.

[jingjtang]

@RoniRos

1. If we consider deaths caused by influenza, pneumonia and covid as different sets. and means Intersection while or means union. So,

   • pneumonia_and_covid_deaths means deaths caused by BOTH pneumonia AND covid.
   • pneumonia_influenza_or_covid_19_deaths means deaths caused by EITHER influenza, pneumonia OR covid

2. As described in their website. I think they are classified based on 'any code'. (not sure whether it is the primary cause)
   COVID-19 deaths are identified using a new ICD–10 code. When COVID-19 is reported as a cause of death – or when it is listed as a “probable” or “presumed” cause — the death is coded as U07.1. This can include cases with or without laboratory confirmation.

[jingjtang]

@korlaxxalrok for automation

[benjaminysmith]

@RoniRos -- is the clarification on naming acceptable, or would you like to change the AND/OR use?

@krivard is there an approver for the correlations above, or is this enough?

[jingjtang]

API documentation PR here