Doctor Visits show an unexpected weekly trend

[nolangormley]

Actual Behavior:

When looking at the data from the Doctor Visits signal, it shows a weekly trend, similar to signals that have weekly reporting (where there is a spike at the beginning of the week).

Expected behavior

Roni and I were looking through this yesterday and didn't seem to understand why this was. Since this is a daily reported signal, we expected it to be much more smooth.

Context

Here's some code to replicate the plot above

import wget

docvisit = wget.download("https://api.covidcast.cmu.edu/epidata/covidcast/csv?signal=doctor-visits:smoothed_cli&start_day=2024-05-29&end_day=2024-08-29&geo_type=nation")
docvisitadj = wget.download("https://api.covidcast.cmu.edu/epidata/covidcast/csv?signal=doctor-visits:smoothed_adj_cli&start_day=2024-05-29&end_day=2024-08-29&geo_type=nation")

df = pd.read_csv("covidcast-doctor-visits-smoothed_cli-2024-05-29-to-2024-08-29.csv")
dfadj = pd.read_csv("covidcast-doctor-visits-smoothed_adj_cli-2024-05-29-to-2024-08-29.csv")

df.time_value = pd.to_datetime(df.time_value, utc=True)
dfadj.time_value = pd.to_datetime(dfadj.time_value, utc=True)
dfadj = dfadj[['time_value', 'value']].rename(columns={'time_value':'time_value', 'value':'valueadj'})

foo = df[['time_value', 'value']].merge(dfadj, on='time_value', how='left')
foo.plot(x='time_value', y=['value', 'valueadj'])

[RoniRos]

Back in July Peter and I noticed this pattern in the "hospital admissions" signals in Texas. Dmitry investigated it and concluded (1) it is already present in the raw signal we receive; and (2) in that signal it is only present in data from Texas but not from other states. The current signal (Doctors Visits) is from the same source. :-(

@dshemetov Did I remember your conclusions correctly? And did we ever file an issue about it? If so, we should link/consolidate them.

[dshemetov]

Hi @RoniRos, sorry this slipped my radar.

As to (1): I only guessed that it wasn't in the raw data in hospital-admissions. I looked at the data with weekday effects removed (unadjusted) and found that it still had this anomaly, but the unadjusted signal is still downstream of a "left Gaussian linear" smoother, which could have a bug. My personal hunch was that a smoother was unlikely to lead to this pattern, but you had the opposite intuition. I didn't try to look for pre-smoother raw data, have had very few extra cycles for this investigation.

As to (2): I didn't do a comprehensive comparison to all the states, but a handful or so, and Texas was the only one with this anomaly.

[RoniRos]

A related observation: the dow (day-of-week) adjusted signal exhibits numerous "jumps" that don't seem to reflect the original data. Perhaps the most egregious example in the above indicator pair (doctor-visits:smoothed_cli and signal=doctor-visits:smoothed_adj_cli) for "United States" is on 2024-03-25 -- 2024-03-28 (M-Th), where the dow-adjusted signal is significantly bumped up but the original doesn't show any changes. It is also visible in individual states at the same time, e.g. PA, CA, TX.
Is this a bug in the dow adjustment algorithm? There shouldn't be a holiday or other calendar effect in late March.

[melange396]

(Epivis link to the time window and signals Roni just referenced)

I think this is probably caused by a bug in an engine used by the solver in the weekday effects adjustment routine, similar to what was noticed in issue #1915. Fixes were made in PR #1966 and PR #1975, and then released to production on July 10, 2024.

[RoniRos]

Thanks George! So have the fixes been applied retroactively? Given the current behavior for that period, I assume the answer is "no". Is it on our stack to apply it at some point? Maybe together with the move to Airflow?

[melange396]

It definitely was on the docket at one point; it must've gotten punted so that we could do it with the new pipeline system.