Synthesize "national" data for nchs-mortality:deaths_covid_incidence_prop

[melange396]

There are currently only "state" specific data points for NCHS Mortality series. That is, only geo_type=state is provided for any of the data with source=nchs-mortality. It would be advantageous for us to have this information aggregated to the national level. We can (presumably) synthesize this by summing numbers from all states to produce a new "nation" data series (for each reference and issue date available).

In cmu-delphi/www-covidcast#1233, on the Covidcast Dashboard, we intend to replace the old and no-longer-updated JHU deaths signal (jhu-csse:deaths_7dav_incidence_prop) with one from NCHS Mortality Data (nchs-mortality:deaths_covid_incidence_prop). The default view of the dashboard uses a geographic perspective of the United States as a whole. Without an available "nation"-level signal for deaths, it shows as "N/A" in plots and numeric text.

According to our signal documentation, the only currently active signals that do not provide "nation"-level data are from the sources nchs-mortality and quidel. Do we want to construct national data for all of these?

[melange396]

It looks like we do something similar for doctor_visits data, by summing across counties to produce "nation" data (among other aggregationss). See:

covidcast-indicators/doctor_visits/delphi_doctor_visits/run.py

Lines 109 to 114 in 39c02fa

	sensor = update_sensor(
	filepath=claims_file,
	startdate=startdate,
	enddate=enddate,
	dropdate=dropdate,
	geo=geo,

covidcast-indicators/doctor_visits/delphi_doctor_visits/update_sensor.py

Line 145 in 39c02fa

mapping_func = geo_map.geo_func[geo.lower()]

covidcast-indicators/doctor_visits/delphi_doctor_visits/geo_maps.py

Line 31 in 39c02fa

"nation": self.county_to_nation}

covidcast-indicators/doctor_visits/delphi_doctor_visits/geo_maps.py

Line 90 in 39c02fa

def county_to_nation(self, data):

[melange396]

(this text is copied from #1912 (comment) ; its more appropriate here)

nchs-mortality national-level data went in last thursday for the first time...

• Good news: it added old dates (though not old issues, but thats probbly fine), and most signals look good to me.
• Less good news: values for "*_prop" national signals are all null.
  • Unfortunately, the one we were interested in for in the dashboard is a prop signal (from Synthesize "national" data for nchs-mortality:deaths_covid_incidence_prop #1906), and it looks like zeroes in the plots.

Did this work for you in your local testing? Since these values are coming out as "NULL", it makes me think the denominator here is 0 or null, which then makes me think that the national population is not getting set properly here.

Also, to make this message go away, we need to mark the nchs-mortality signals as having national-level data in the spreadsheet and then get it transferred to the csv. We can take care of that after the signals are properly acquired.