doctor-visits.md

title	Doctor Visits
parent	Data Sources and Signals
grand_parent	Main Endpoint (COVIDcast)
nav_order	1

Heads up: This COVIDcast source is part of the legacy V4 API, which is being phased out. An actively maintained equivalent is available in V5 under the source claims_data_outpatient. See the V4 to V5 Migration Guide for full details. {: .warning }

Doctor Visits

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Attribute	Details
Source Name	doctor-visits
Data Source	Health system partners
Geographic Levels	State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see geography coding docs)
Temporal Granularity	Daily (see date format docs)
Reporting Cadence	Daily
Date of last data revision:	November 9, 2020 (see data revision docs)
Temporal Scope Start	2020-02-01
License	CC BY

Changelog

Click to expand

See COVIDcast Signal Changes for general information about how we track changes to signals.

November 9, 2020

We went from a custom geo-mapping file (for aggregating from county->(msa, hrr, state)) to a central geo file based on rigorously sourced US census data.

Overview

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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 Earliest date available: 2020-02-01
smoothed_adj_cli	Same, but with systematic day-of-week effects removed; see details below Earliest date available: 2020-02-01

Table of Contents

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1. TOC {:toc}

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

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

Note on Uncertainty: The standard error formula below represents the theoretical error of the binomial proportion. However, due to the smoothing and day-of-week adjustments applied later in the pipeline, the actual standard error in the final signal will differ.

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

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.

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 that include the most recent data reports. This means that a reported estimate for, June 10th, may first be available in the API on June 14th and subsequently revised on June 16th.

As insurance claims are available at a significant and variable latency, the signal experiences heavy backfill with data delayed for a couple of weeks. We expect estimates available for the most recent 5-7 days to change substantially in later data revisions (having a median delta of 10% or more). Estimates for dates more than 50 days in the past are expected to remain fairly static (having a median delta of 1% or less), as most major revisions have already occurred.

See our blog post for more information on backfill.

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 and sample sizes are not available for this data source.

Due to changes in medical-seeking behavior on holidays, this data source has upward spikes in the fraction of doctor's visits that are COVID-related around major holidays (e.g. Memorial Day, July 4, Labor Day, etc.). These spikes are not necessarily indicative of a true increase of COVID-like illness in a location.

Note that due to local differences in health record-keeping practices, estimates are not always comparable across locations. We are currently working on adjustments to correct this spatial bias.

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.