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Merge pull request #770 from cmu-delphi/krivard/no-combo-cases
Remove combo cases from active signals
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‎docs/api/covidcast-signals/indicator-combination-inactive.md

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@@ -200,3 +200,30 @@ The resampling method for each input source is as follows:
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the reported proportion and sample size.
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* *Google Health Trends:* Because we do not have access to the sampling
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distribution, we do not resample this signal.
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## Compositional Signals: Confirmed Cases and Deaths
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* **Earliest issue available:** 7 July 2020
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* **Number of data revisions since 19 May 2020:** 1
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* **Date of last change:** [12 October 2020](../covidcast_changelog.md#indicator-combination)
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* **Available for:** county, msa, hrr, state (see [geography coding docs](../covidcast_geography.md))
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* **Time type:** day (see [date format docs](../covidcast_times.md))
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These signals combine the cases and deaths data from JHU and USA Facts. This is
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a straight composition: the signals below use the [JHU signal data](jhu-csse.md)
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for Puerto Rico, and the [USA Facts signal data](usa-facts.md) everywhere else.
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Consult each signal's documentation for information about geographic reporting,
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backfill, and other limitations.
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These signals were updated daily until November 18, 2021.
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| Signal | 7-day average signal | Description |
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| --- | --- | --- |
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| `confirmed_cumulative_num` | | Cumulative number of confirmed COVID-19 cases <br/> **Earliest date available:** 2020-02-20 |
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| `confirmed_cumulative_prop` | | Cumulative number of confirmed COVID-19 cases per 100,000 population <br/> **Earliest date available:** 2020-02-20 |
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| `confirmed_incidence_num` | `confirmed_7dav_incidence_num` | Number of new confirmed COVID-19 cases, daily <br/> **Earliest date available:** 2020-02-20 |
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| `confirmed_incidence_prop` | `confirmed_7dav_incidence_prop` | Number of new confirmed COVID-19 cases per 100,000 population, daily <br/> **Earliest date available:** 2020-02-20 |
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| `deaths_cumulative_num` | | Cumulative number of confirmed deaths due to COVID-19 <br/> **Earliest date available:** 2020-02-20 |
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| `deaths_cumulative_prop` | | Cumulative number of confirmed due to COVID-19, per 100,000 population <br/> **Earliest date available:** 2020-02-20 |
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| `deaths_incidence_num` | `deaths_7dav_incidence_num` | Number of new confirmed deaths due to COVID-19, daily <br/> **Earliest date available:** 2020-02-20 |
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| `deaths_incidence_prop` | `deaths_7dav_incidence_prop` | Number of new confirmed deaths due to COVID-19 per 100,000 population, daily <br/> **Earliest date available:** 2020-02-20 |

‎docs/api/covidcast-signals/indicator-combination.md

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‎docs/api/covidcast_licensing.md

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* [Doctor Visits](covidcast-signals/doctor-visits.md)
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* [Hospital Admissions](covidcast-signals/hospital-admissions.md)
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* [Indicator Combination](covidcast-signals/indicator-combination.md): signals
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* [Indicator Combination](covidcast-signals/indicator-combination-inactive.md): signals
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with names beginning `nmf_*`
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* [Quidel](covidcast-signals/quidel.md)
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* [Symptom Surveys](covidcast-signals/fb-survey.md)
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published here subject to the original license provided by the source:
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* [Google Health Trends](covidcast-signals/ght.md)
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* [Indicator Combination](covidcast-signals/indicator-combination.md): cases and
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* [Indicator Combination](covidcast-signals/indicator-combination-inactive.md): cases and
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deaths signals
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* [JHU Cases and Deaths](covidcast-signals/jhu-csse.md)
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* [SafeGraph Mobility](covidcast-signals/safegraph.md)

‎docs/api/covidcast_signals.md

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| Early Indicators | COVID-Like Symptoms in Community | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_hh_cmnty_cli` |
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| Late Indicators | COVID Antigen Test Positivity (Quidel) | [`quidel`](covidcast-signals/quidel.md) | `covid_ag_smoothed_pct_positive` |
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| Late Indicators | Claims-Based COVID Hospital Admissions | [`hospital-admissions`](covidcast-signals/hospital-admissions.md) | `smoothed_adj_covid19_from_claims` |
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| Late Indicators | Cases | [`indicator-combination`](covidcast-signals/indicator-combination.md) | `confirmed_7dav_incidence_num` |
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| Late Indicators | Cases per 100,000 People | [`indicator-combination`](covidcast-signals/indicator-combination.md) | `confirmed_7dav_incidence_prop` |
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| Late Indicators | Deaths | [`indicator-combination`](covidcast-signals/indicator-combination.md) | `deaths_7dav_incidence_num` |
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| Late Indicators | Deaths per 100,000 People | [`indicator-combination`](covidcast-signals/indicator-combination.md) | `deaths_7dav_incidence_prop` |
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| Late Indicators | Cases | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `confirmed_7dav_incidence_num` |
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| Late Indicators | Cases per 100,000 People | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `confirmed_7dav_incidence_prop` |
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| Late Indicators | Deaths | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `deaths_7dav_incidence_num` |
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| Late Indicators | Deaths per 100,000 People | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `deaths_7dav_incidence_prop` |
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## All Available Sources and Signals
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‎src/server/endpoints/covidcast_utils/db_signals.csv

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Discontinued October 1, 2020.",day,Date,Percentage,percent,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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hospital-admissions,smoothed_covid19_from_claims,FALSE,smoothed_covid19_from_claims,FALSE,COVID-19 Admissions (Claims),TRUE,Estimated percentage of new hospital admissions with COVID-associated diagnoses,"{short_description}, based on counts of claims from health system partners, smoothed in time using a Gaussian linear smoother.",day,Date,Percentage,percent,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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hospital-admissions,smoothed_covid19_from_claims,TRUE,smoothed_adj_covid19_from_claims,FALSE,{base_name} (Day-adjusted),TRUE,,"{base_short_description}, based on counts of claims from health system partners, smoothed in time using a Gaussian linear smoother, and adjusted to reduce day-of-week effects.",day,Date,Percentage,percent,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,FALSE,confirmed_cumulative_num,FALSE,Confirmed COVID Cases (Cumulative),TRUE,Cumulative confirmed COVID cases,Confirmed COVID-19 cases as reported by [USAFacts](https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/) and [JHU-CSSE](https://github.com/CSSEGISandData/COVID-19),day,Date,Value,count,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_7dav_incidence_num,TRUE,"Confirmed COVID Cases (Daily new, 7-day average)",TRUE,"Daily new confirmed COVID cases, 7-day average ",,day,Date,Value,count,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_7dav_incidence_prop,FALSE,"Confirmed COVID Cases (Daily new, 7-day average, per 100k people)",TRUE,"Daily new confirmed COVID cases, 7-day average, per 100k people",,day,Date,Value,per100k,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_cumulative_prop,FALSE,"Confirmed COVID Cases (Cumulative, per 100k people)",TRUE,"Cumulative confirmed COVID cases, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_incidence_num,TRUE,Confirmed COVID Cases (Daily new),TRUE,Daily new confirmed COVID cases,,day,Date,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_incidence_prop,FALSE,"Confirmed COVID Cases (Daily new, per 100k people)",TRUE,"Daily new confirmed COVID cases, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,FALSE,deaths_cumulative_num,FALSE,Confirmed COVID Deaths (Cumulative),TRUE,Cumulative confirmed COVID deaths,Confirmed COVID-19 deaths as reported by [USAFacts](https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/) and [JHU-CSSE](https://github.com/CSSEGISandData/COVID-19),day,Date,Value,count,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_7dav_incidence_num,TRUE,"Confirmed COVID Deaths (Daily new, 7-day average)",TRUE,"Daily new confirmed COVID deaths, 7-day average ",,day,Date,Value,count,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_7dav_incidence_prop,FALSE,"Confirmed COVID Deaths (Daily new, 7-day average, per 100k people)",TRUE,"Daily new confirmed COVID deaths, 7-day average, per 100k people",,day,Date,Value,per100k,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_cumulative_prop,FALSE,"Confirmed COVID Deaths (Cumulative, per 100k people)",TRUE,"Cumulative confirmed COVID deaths, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_incidence_num,TRUE,Confirmed COVID Deaths (Daily new),TRUE,Daily new confirmed COVID deaths,,day,Date,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_incidence_prop,FALSE,"Confirmed COVID Deaths (Daily new, per 100k people)",TRUE,"Daily new confirmed COVID deaths, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,FALSE,confirmed_cumulative_num,FALSE,Confirmed COVID Cases (Cumulative),FALSE,Cumulative confirmed COVID cases,Confirmed COVID-19 cases as reported by [USAFacts](https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/) and [JHU-CSSE](https://github.com/CSSEGISandData/COVID-19),day,Date,Value,count,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_7dav_incidence_num,TRUE,"Confirmed COVID Cases (Daily new, 7-day average)",FALSE,"Daily new confirmed COVID cases, 7-day average ",,day,Date,Value,count,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_7dav_incidence_prop,FALSE,"Confirmed COVID Cases (Daily new, 7-day average, per 100k people)",FALSE,"Daily new confirmed COVID cases, 7-day average, per 100k people",,day,Date,Value,per100k,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_cumulative_prop,FALSE,"Confirmed COVID Cases (Cumulative, per 100k people)",FALSE,"Cumulative confirmed COVID cases, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_incidence_num,TRUE,Confirmed COVID Cases (Daily new),FALSE,Daily new confirmed COVID cases,,day,Date,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,confirmed_cumulative_num,TRUE,confirmed_incidence_prop,FALSE,"Confirmed COVID Cases (Daily new, per 100k people)",FALSE,"Daily new confirmed COVID cases, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,FALSE,deaths_cumulative_num,FALSE,Confirmed COVID Deaths (Cumulative),FALSE,Cumulative confirmed COVID deaths,Confirmed COVID-19 deaths as reported by [USAFacts](https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/) and [JHU-CSSE](https://github.com/CSSEGISandData/COVID-19),day,Date,Value,count,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_7dav_incidence_num,TRUE,"Confirmed COVID Deaths (Daily new, 7-day average)",FALSE,"Daily new confirmed COVID deaths, 7-day average ",,day,Date,Value,count,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_7dav_incidence_prop,FALSE,"Confirmed COVID Deaths (Daily new, 7-day average, per 100k people)",FALSE,"Daily new confirmed COVID deaths, 7-day average, per 100k people",,day,Date,Value,per100k,late,bad,TRUE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_cumulative_prop,FALSE,"Confirmed COVID Deaths (Cumulative, per 100k people)",FALSE,"Cumulative confirmed COVID deaths, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_incidence_num,TRUE,Confirmed COVID Deaths (Daily new),FALSE,Daily new confirmed COVID deaths,,day,Date,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-cases-deaths,deaths_cumulative_num,TRUE,deaths_incidence_prop,FALSE,"Confirmed COVID Deaths (Daily new, per 100k people)",FALSE,"Daily new confirmed COVID deaths, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
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indicator-combination-nmf,nmf_day_doc_fbc_fbs_ght,nmf_day_doc_fbc_fbs_ght,nmf_day_doc_fbc_fbs_ght,FALSE,NMF Combination (with community symptoms),FALSE,Rank-1 NMF approximation to reconstruct 4 other signals.,"This signal uses a rank-1 approximation, from a nonnegative matrix factorization approach, to identify an underlying signal that best reconstructs the Doctor Visits (smoothed_adj_cli), Facebook Symptoms surveys (smoothed_cli), Facebook Symptoms in Community surveys (smoothed_hh_cmnty_cli), and Search Trends (smoothed_search) indicators. It does not include official reports (cases and deaths from the jhu-csse source). Higher values of the combined signal correspond to higher values of the other indicators, but the scale (units) of the combination is arbitrary. Note that the Search Trends source is not available at the county level, so county values of this signal do not use it.
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Discontinued March 17, 2021.",day,Date,Value,raw,early,bad,FALSE,FALSE,FALSE,TRUE,FALSE,

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