diff --git a/docs/api/covidcast-signals/chng.md b/docs/api/covidcast-signals/chng.md index 3dac39c31..be87fc3b4 100644 --- a/docs/api/covidcast-signals/chng.md +++ b/docs/api/covidcast-signals/chng.md @@ -26,6 +26,8 @@ commercial purposes. | --- | --- | | `smoothed_outpatient_covid` | Estimated percentage of outpatient doctor visits with confirmed COVID-19, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time using a Gaussian linear smoother | | `smoothed_adj_outpatient_covid` | Same, but with systematic day-of-week effects removed; see [details below](#day-of-week-adjustment) | +| `smoothed_outpatient_cli` | Estimated percentage of outpatient doctor visits primarily about COVID-related symptoms, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time using a Gaussian linear smoother | +| `smoothed_adj_outpatient_cli` | Same, but with systematic day-of-week effects removed; see [details below](#day-of-week-adjustment) | ## Table of contents {: .no_toc .text-delta} @@ -64,15 +66,38 @@ not necessarily indicative of a true increase of COVID-19 in a location. ## Qualifying Conditions -We receive data on the following two categories of counts: +We receive data on the following six categories of counts: - Denominator: Daily count of all unique outpatient visits. - Covid: Daily count of all unique visits with primary ICD-10 code in any of: {U07.1, B97.21, or B97.29}. +- COVID-like: Daily count of all unique outpatient visits with primary ICD-10 code + of any of: {U07.1, U07.2, B97.29, J12.81, Z03.818, B34.2, J12.89}. +- Flu-like: Daily count of all unique outpatient visits with primary ICD-10 code + of any of: {J22, B34.9}. 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: {Z20.828, J12.9}. 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. + +For the COVID signal, we consider only the *Denominator* and *Covid* counts. + +For the CLI signal, 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 +### COVID Illness + +The following estimation method is used for the `*_outpatient_covid` signals. For a fixed location $$i$$ and time $$t$$, let $$Y_{it}$$ denote the Covid counts and let $$N_{it}$$ be the @@ -83,6 +108,22 @@ $$ \hat p_{it} = 100 \cdot \frac{Y_{it}}{N_{it}} $$ +### COVID-Like Illness + +The following estimation method is used for the `*_outpatient_cli` signals. + +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 + +$$ +\hat p_{it} = 100 \cdot \frac{Y_{it}^{\text{Covid-like}} + + \left((Y_{it}^{\text{Flu-like}} + Y_{it}^{\text{Mixed}}) - + Y_{it}^{\text{Flu}}\right)}{N_{it}} +$$ + ### Day-of-Week Adjustment The fraction of visits due to COVID-19 is dependent on the day of the week. On @@ -131,6 +172,10 @@ $$\dot{Y}_{it} = Y_{it} / \alpha_{wd(t)}.$$ We then use these adjusted counts to estimate the COVID-19 percentage as described above. +For the CLI indicator, we apply the same method to the numerator $$Y_{it} = +Y_{it}^{\text{Covid-like}} + \left((Y_{it}^{\text{Flu-like}} + +Y_{it}^{\text{Mixed}}) - Y_{it}^{\text{Flu}}\right).$$ + ### Backwards Padding To help with the reporting delay, we perform the following simple