NSSP data for HRRs is not summed properly

[melange396]

it is computed with a basic sum instead of a weighted one like the other geo types we aggregate ourselves. as a result the scale is off and can be >100% (see nssp:pct_ed_visits_influenza @hrr:366 )

[minhkhul]

Probably adjust some wording/add warning in geomapper here too. This original geomap instruction was why I implemented custom weighting for msa and hhs but not hrr.

covidcast-indicators/_delphi_utils_python/delphi_utils/geomap.py

Lines 99 to 104 in 454ac56

	Example 2: to replace a geocode column with a new one, aggregating the data
	with weights:
	> gmpr = GeoMapper()
	> df = gmpr.replace_geocode(df, "fips", "zip",
	from_col="fips", new_col="geo_id",
	date_col="timestamp", dropna=False)

[melange396]

I just did another read-through of some GeoMapper code... It looks like .replace_geocode() can/should produce weighted sums for certain geo-level conversions (through a sneaky and convoluted path), but the precomputed fips-->hrr weights do not add up the way they should. Using your other approach that calls .aggregate_by_weighted_sum() w/ population should get around this.

[dshemetov]

I'm pretty familiar with GeoMapper, having written much of the current core logic in #217 and in #1960, so I figure I should provide some context. These functions contain a lot of implicit assumptions about the data, by the way they handle the missingness edge case, and these assumptions are hard to convey succinctly (more on that below). I don't think the fips->hrr weights are wrong. I think the TL;DR of the problem here is that

• replace_geocode() is appropriate for aggregating unnormalized counts data and implicitly considers missing geos to be zero
• aggregate_by_weighted_sum() is intended for normalized data and implicitly extrapolates to missing geos from present neighbor geos

We should definitely use aggregate_by_weighted_sum() in this code path. And I should improve the GeoMapper docstring. Maybe add a "GeoMapper by example" notebook too.

Context:

("Source geo" and "target geo" below refer to the geos being translated. So for the bug in question, source geos are fips and target geos are hrrs).

NSSP data is all percent of state ED visits and it's full of incomplete reporting (i.e. not every county reports values), so (a) adding values across separate source geos doesn't make sense without some sort of population adjustment, (b) we need a strategy to handle missingness in source geos. Since the target geo needs to also report a percentage, it has to be normalized after aggregating and we're forced into a modeling choice by our choice of denominator:

• if you normalize by the total population of the target geo, but the numerator only added present source geos, then that translates to an implicit zero-fill assumption on the missing source geos
• if you normalize by the population of only the present source geos, then that translates to an implicit extrapolation from the present geos

David and I settled on the latter choice, since we figured that assuming nearby missing geos are similar is more correct than assuming they are zero. He wrote the original aggregate_by_weighted_sum() for this purpose and I generalized and ported it to GeoMapper. In hindsight, and as these things tend to go, we spent all our time getting the functionality right and no time choosing a good function name, so we ended up with this too-generic-to-be-descriptive thing 🙃.

[melange396]

Reopening because this still needs some sort of "patching-like" action, either deleting the erroneous data or overwriting it with correct data, depending on available options (im not familiar enough with the issuance and revision behavior of the source data nor with our backups of it off the top of my head).

[minhkhul]

todo:

• delete old hrr data
  • took ~1hr late last night
  • DELETE epimetric_x FROM epimetric_x JOIN signal_dim USING (signal_key_id) JOIN geo_dim USING (geo_key_id) WHERE source='nssp' AND geo_type='hrr';
• release covidcast indicators to the fix is applied for future runs.
  • done in Release covidcast-indicators 0.3.62 #2134
• patch old hrr data