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Doctor Visits

  • Source name: doctor-visits
  • Number of data revisions since 19 May 2020: 0
  • Date of last change: Never
  • Available for: county, hrr, msa, state (see geography coding docs)

This data source is based on information about outpatient visits, provided to us by health system partners. Using this outpatient data, we estimate the percentage of COVID-related doctor’s visits in a given location, on a given day.

Signal Description
smoothed_cli Estimated percentage of outpatient doctor visits primarily about COVID-related symptoms, based on data from health system partners, smoothed in time using a Gaussian linear smoother
smoothed_adj_cli Same, but with systematic day-of-week effects removed; see details below

Table of contents

  1. Lag and Backfill
  2. Limitations
  3. Qualifying Conditions
  4. Estimation
    1. COVID-Like Illness
    2. Day-of-Week Adjustment
    3. Backwards Padding
    4. Smoothing

Lag and Backfill

Note that because doctor’s visits may be reported to the health system partners several days after they occur, these signals are typically available with several days of lag. This means that estimates for a specific day are only available several days later.

The amount of lag in reporting can vary, and not all visits are reported with the same lag. After we first report estimates for a specific date, further data may arrive about outpatients visits on that date. When this occurs, we issue new estimates for those dates. This means that a reported estimate for, say, June 10th may first be available in the API on June 14th and subsequently revised on June 16th.

Limitations

This data source is based on outpatient visit data provided to us by health system partners. The partners can report on a portion of United States outpatient doctor’s visits, but not all of them, and so this source only represents those visits known to them. Their coverage may vary across the United States.

Standard errors are not available for this data source.

Qualifying Conditions

We receive data on the following five categories of counts:

  • Denominator: Daily count of all unique outpatient visits.
  • COVID-like: Daily count of all unique outpatient visits with primary ICD-10 code of any of: {U071, U072, B9729, J1281, Z03818, B342, J1289}.
  • Flu-like: Daily count of all unique outpatient visits with primary ICD-10 code of any of: {J22, B349}. The occurrence of these codes in an area is correlated with that area’s historical influenza activity, but are diagnostic codes not specific to influenza and can appear in COVID-19 cases.
  • Mixed: Daily count of all unique outpatient visits with primary ICD-10 code of any of: {Z20828, J129}. The occurance of these codes in an area is correlated to a blend of that area’s COVID-19 confirmed case counts and influenza behavior, and are not diagnostic codes specific to either disease.
  • Flu: Daily count of all unique outpatient visits with primary ICD-10 code of any of: {J09*, J10*, J11*}. The asterisk * indicates inclusion of all subcodes. This set of codes are assigned to influenza viruses.

If a patient has multiple visits on the same date (and hence multiple primary ICD-10 codes), then we will only count one of and in descending order: Flu, COVID-like, Flu-like, Mixed. This ordering tries to account for the most definitive confirmation, e.g. the codes assigned to Flu are only used for confirmed influenza cases, which are unrelated to the COVID-19 coronavirus.

Estimation

COVID-Like Illness

For a fixed location \(i\) and time \(t\), let \(Y_{it}^{\text{Covid-like}}\), \(Y_{it}^{\text{Flu-like}}\), \(Y_{it}^{\text{Mixed}}\), \(Y_{it}^{\text{Flu}}\) denote the correspondingly named ICD-filtered counts and let \(N_{it}\) be the total count of visits (the Denominator). Our estimate of the CLI percentage is given by

\[\hat p_{it} = 100 \cdot \frac{Y_{it}^{\text{Covid-like}} + \left((Y_{it}^{\text{Flu-like}} + Y_{it}^{\text{Mixed}}) - Y_{it}^{\text{Flu}}\right)}{N_{it}}\]

The estimated standard error is:

\[\widehat{\text{se}}(\hat{p}_{it}) = 100 \sqrt{\frac{\frac{\hat{p}_{it}}{100}(1-\frac{\hat{p}_{it}}{100})}{N_{it}}}.\]

Note the quantity above is not going to be correct for multiple reasons: smoothing/day of week adjustments/etc.

Day-of-Week Adjustment

The fraction of visits due to CLI is dependent on the day of the week. On weekends, doctors see a higher percentage of acute conditions, so the percentage of CLI is higher. Each day of the week has a different behavior, and if we do not adjust for this effect, we will not be able to meaningfully compare the doctor visits signal across different days of the week. We use a Poisson regression model to produce a signal adjusted for this effect.

We assume that this weekday effect is multiplicative. For example, if the underlying rate of CLI on each Monday was the same as the previous Sunday, then the ratio between the doctor visit signals on Sunday and Monday would be a constant. Formally, we assume that

\[\begin{aligned} \mathbb{E}[Y_{it}] &= \mu_t\\ \log \mu_t &= \alpha_{\text{wd}(t)} + \phi_t, \end{aligned}\]

where \(Y_{it}\) is the observed doctor visits percentage of CLI at time \(t\), \(\text{wd}(t) \in \{0, \dots, 6\}\) is the day-of-week of time \(t\), \(\alpha_{\text{wd}(t)}\) is the corresponding weekday correction, and \(\phi_t\) is the corrected doctor visits percentage of CLI at time \(t\).

For simplicity, we assume that the weekday parameters do not change over time or location. To fit the \(\alpha\) parameters, we minimize the following convex objective function:

\[f(\alpha, \phi | \mu) = -\log \ell (\alpha,\phi|\mu) + \lambda ||\Delta^3 \phi||_1\]

where \(\ell\) is the Poisson likelihood and \(\Delta^3 \phi\) is the third differences of \(\phi\). For identifiability, we constrain the sum of \(\alpha\) to be zero by setting Sunday’s fixed effect to be the negative sum of the other weekdays. The penalty term encourages the \(\phi\) curve to be smooth and produces meaningful \(\alpha\) values.

Once we have estimated values for \(\alpha\) for each type of count \(k\) in {COVID-like, Flu-like, Mixed, Flu}, we obtain the adjusted count

\[\dot{Y}_{it}^k = Y_{it}^k / \alpha_{wd(t)}.\]

We then use these adjusted counts to estimate the CLI percentage as described above.

Backwards Padding

To help with the reporting delay, we perform the following simple correction on each location. At each time \(t\), we consider the total visit count. If the value is less than a minimum sample threshold, we go back to the previous time \(t-1\), and add this visit count to the previous total, again checking to see if the threshold has been met. If not, we continue to move backwards in time until we meet the threshold, and take the estimate at time \(t\) to be the average over the smallest window that meets the threshold. We enforce a hard stop to consider only the past 7 days, if we have not yet met the threshold during that time bin, no estimate will be produced. If, for instance, at time \(t\), the minimum sample threshold is already met, then the estimate only contains data from time \(t\). This is a dynamic-length moving average, working backwards through time. The threshold is set at 500 observations.

Smoothing

To help with variability, we also employ a local linear regression filter with a Gaussian kernel. The bandwidth is fixed to approximately cover a rolling 7 day window, with the highest weight placed on the right edge of the window (the most recent timepoint). Given this smoothing step, the standard error estimate shown above is not exactly correct, as the calculation is done post-smoothing.