move inactive signals to main signal list

Combine inactive quidel and active quidel. Rename "Other Endpoints". Developer support section creation and organization.
cmu-delphi · Jul 23, 2024 · c8614db · c8614db
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diff --git a/docs/api/README.md b/docs/api/README.md
@@ -1,10 +1,10 @@
 ---
-title: Other Endpoints (COVID-19 and Other Diseases)
-nav_order: 3
+title: Other Endpoints
 has_children: true
+nav_order: 3
 ---
 
-# Epidata API (Other Diseases)
+# Other Endpoints
 
 This is the home of [Delphi](https://delphi.cmu.edu/)'s epidemiological data
 API for tracking epidemics such as influenza, dengue, and norovirus. Note that

diff --git a/docs/api/api_keys.md b/docs/api/api_keys.md
@@ -1,7 +1,7 @@
 ---
 title: API Keys
+parent: Epidata API Intro
 nav_order: 1
-has_children: true
 ---
 
 # Epidata API Keys

diff --git a/docs/api/cdc.md b/docs/api/cdc.md
@@ -1,6 +1,6 @@
 ---
 title: CDC
-parent: Other Endpoints (COVID-19 and Other Diseases)
+parent: Other Endpoints
 ---
 
 # CDC

diff --git a/docs/api/client_libraries.md b/docs/api/client_libraries.md
@@ -1,7 +1,7 @@
 ---
 title: Epidata API Client Libraries
-parent: Other Endpoints (COVID-19 and Other Diseases)
-nav_order: 1
+parent: Epidata API Intro
+nav_order: 2
 ---
 
 # Epidata API Client Libraries

diff --git a/docs/api/covid_hosp.md b/docs/api/covid_hosp.md
@@ -1,6 +1,6 @@
 ---
 title: COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries
-parent: Other Endpoints (COVID-19 and Other Diseases)
+parent: Other Endpoints
 ---
 
 # COVID-19 Hospitalization by State

diff --git a/docs/api/covid_hosp_facility.md b/docs/api/covid_hosp_facility.md
@@ -1,6 +1,6 @@
 ---
 title: COVID-19 Reported Patient Impact and Hospital Capacity by Facility
-parent: Other Endpoints (COVID-19 and Other Diseases)
+parent: Other Endpoints
 ---
 
 # COVID-19 Hospitalization by Facility

diff --git a/docs/api/covid_hosp_facility_lookup.md b/docs/api/covid_hosp_facility_lookup.md
@@ -1,6 +1,6 @@
 ---
 title: COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup
-parent: Other Endpoints (COVID-19 and Other Diseases)
+parent: Other Endpoints
 ---
 
 # COVID-19 Hospitalization: Facility Lookup

diff --git a/docs/api/covidcast-signals/covid-act-now.md b/docs/api/covidcast-signals/covid-act-now.md
@@ -1,6 +1,6 @@
 ---
-title: COVID Act Now
-parent: Inactive Signals
+title: COVID Act Now (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast-signals/dsew-cpr.md b/docs/api/covidcast-signals/dsew-cpr.md
@@ -1,6 +1,6 @@
 ---
-title: Data Strategy and Execution Workgroup Community Profile Report
-parent: Inactive Signals
+title: Data Strategy and Execution Workgroup Community Profile Report (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast-signals/fb-survey.md b/docs/api/covidcast-signals/fb-survey.md
@@ -1,6 +1,6 @@
 ---
-title: COVID-19 Trends and Impact Survey
-parent: Inactive Signals
+title: COVID-19 Trends and Impact Survey (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast-signals/google-survey.md b/docs/api/covidcast-signals/google-survey.md
@@ -1,6 +1,6 @@
 ---
-title: Google Symptom Surveys
-parent: Inactive Signals
+title: Google Symptom Surveys (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast-signals/google-symptoms.md b/docs/api/covidcast-signals/google-symptoms.md
@@ -1,5 +1,5 @@
 ---
-title: Google Search Trends symptoms dataset
+title: Google Search Trends Symptoms (inactive)
 parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---

diff --git a/docs/api/covidcast-signals/hhs.md b/docs/api/covidcast-signals/hhs.md
@@ -1,5 +1,5 @@
 ---
-title: Department of Health & Human Services
+title: Department of Health & Human Services (inactive)
 parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---

diff --git a/docs/api/covidcast-signals/indicator-combination b/docs/api/covidcast-signals/indicator-combination
@@ -1,6 +1,6 @@
 ---
-title: Indicator Combination
-parent: Inactive Signals
+title: Indicator Combination (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast-signals/jhu-csse.md b/docs/api/covidcast-signals/jhu-csse.md
@@ -1,6 +1,6 @@
 ---
-title: JHU Cases and Deaths
-parent: Inactive Signals
+title: JHU Cases and Deaths (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast-signals/quidel.md b/docs/api/covidcast-signals/quidel.md
@@ -7,8 +7,6 @@ grand_parent: COVIDcast Main Endpoint
 # Quidel
 {: .no_toc}
 
-* **Source name:** `quidel`
-
 ## Table of Contents
 {: .no_toc .text-delta}
 
@@ -17,15 +15,18 @@ grand_parent: COVIDcast Main Endpoint
 
 ## Accessibility: Delphi-internal only
 
-## COVID-19 Tests
+## Quidel COVID-19 Tests
 
+* **Source name:** `quidel`
 * **Earliest issue available:** July 29, 2020 
 * **Number of data revisions since May 19, 2020:** 1
 * **Date of last change:** October 22, 2020
 * **Available for:** county, hrr, msa, state, HHS, nation (see [geography coding docs](../covidcast_geography.md))
 * **Time type:** day (see [date format docs](../covidcast_times.md))
 * **License:** [CC BY](../covidcast_licensing.md#creative-commons-attribution)
 
+### Overview
+
 Data source based on COVID-19 Antigen tests, provided to us by Quidel, Inc. When
 a patient (whether at a doctor’s office, clinic, or hospital) has COVID-like
 symptoms, doctors may order an antigen test. An antigen test can detect parts of
@@ -159,5 +160,58 @@ not enough samples can be filled in from the parent state for smoothed signals s
 no data is reported for that area on that day; an API query for all reported geographic areas on
 that day will not include it.
 
-## Flu Tests
-These signals are inactive. They were updated until May 19, 2020. Documentation is still available on the [Quidel influenza page](quidel-flu.md).
+## Quidel Flu Tests (inactive)
+
+These signals are inactive. They were updated until May 19, 2020.
+
+* **Source name: `quidel`
+* **Earliest issue available:** April 29, 2020
+* **Last issued:** May 19, 2020
+* **Number of data revisions since May 19, 2020:** 0
+* **Date of last change:** Never
+* **Available for:** msa, state (see [geography coding docs](../covidcast_geography.md))
+* **Time type:** day (see [date format docs](../covidcast_times.md))
+
+### Overview
+
+Data source based on flu lab tests, provided to us by Quidel, Inc. When a
+patient (whether at a doctor’s office, clinic, or hospital) has COVID-like
+symptoms, doctors may perform a flu test to rule out seasonal flu (influenza),
+because these two diseases have similar symptoms. Using this lab test data, we
+estimate the total number of flu tests per medical device (a measure of testing
+frequency), and the percentage of flu tests that are *negative* (since ruling
+out flu leaves open another cause---possibly covid---for the patient's
+symptoms), in a given location, on a given day.
+
+The number of flu tests conducted in individual counties can be quite small, so
+we do not report these signals at the county level.
+
+The flu test data is no longer updated as of May 19, 2020, as the number of flu
+tests conducted during the summer (outside of the normal flu season) is quite
+small.
+
+| Signal | Description |
+| --- | --- |
+| `raw_pct_negative` | The percentage of flu tests that are negative, suggesting the patient's illness has another cause, possibly COVID-19 <br/> **Earliest date available:** 2020-01-31 |
+| `smoothed_pct_negative` | Same as above, but smoothed in time <br/> **Earliest date available:** 2020-01-31 |
+| `raw_tests_per_device` | The average number of flu tests conducted by each testing device; measures volume of testing <br/> **Earliest date available:** 2020-01-31 |
+| `smoothed_tests_per_device` | Same as above, but smoothed in time <br/> **Earliest date available:** 2020-01-31 | 
+
+### Parameters
+
+#### Required
+
+| Parameter | Description | Type |
+| --- | --- | --- |
+| `auth` | password | string |
+| `epiweeks` | epiweeks | `list` of epiweeks |
+| `locations` | locations | `list` of `hhs<#>` [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt) labels |
+
+### Response
+
+| Field     | Description                                                     | Type             |
+|-----------|-----------------------------------------------------------------|------------------|
+| `result`  | result code: 1 = success, 2 = too many results, -2 = no results | integer          |
+| `epidata` | list of results                                                 | array of objects |
+| ...       | ...                                                             | ...              | <!-- TODO -->
+| `message` | `success` or error message                                      | string           |
diff --git a/docs/api/covidcast-signals/safegraph.md b/docs/api/covidcast-signals/safegraph.md
@@ -1,6 +1,6 @@
 ---
-title: SafeGraph
-parent: Inactive Signals
+title: SafeGraph (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast-signals/usa-facts.md b/docs/api/covidcast-signals/usa-facts.md
@@ -1,6 +1,6 @@
 ---
-title: USAFacts Cases and Deaths
-parent: Inactive Signals
+title: USAFacts Cases and Deaths (inactive)
+parent: Data Sources and Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 

diff --git a/docs/api/covidcast.md b/docs/api/covidcast.md
@@ -86,8 +86,43 @@ including confirmed cases, symptom-related search queries, hospitalizations,
 outpatient doctor's visits, and other sources. Many of these are publicly
 available *only* through the COVIDcast API.
 
-The [signals documentation](covidcast_signals.md) describes all available
-sources and signals.
+Delphi's COVID-19 Surveillance Streams data includes the following data sources.
+Data from most of these sources is typically updated daily. You can use the
+[`covidcast_meta`](covidcast_meta.md) endpoint to get summary information
+about the ranges of the different attributes for the different data sources.
+
+The API for retrieving data from these sources is described in the
+[COVIDcast endpoint documentation](covidcast.md). Changes and corrections to
+data from this endpoint are listed in the [changelog](covidcast_changelog.md).
+
+To obtain many of these signals and update them daily, Delphi has written
+extensive software to obtain data from various sources, aggregate the data,
+calculate statistical estimates, and format the data to be shared through the
+COVIDcast endpoint of the Delphi Epidata API. This code is 
+[open source and available on GitHub](https://github.com/cmu-delphi/covidcast-indicators),
+and contributions are welcome.
+
+### COVIDcast Dashboard Signals
+
+The following signals are currently displayed on [the public COVIDcast
+dashboard](https://delphi.cmu.edu/covidcast/):
+
+| Kind | Name | Source | Signal |
+|---|---|---|---|
+| Public Behavior | People Wearing Masks | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_wwearing_mask_7d` |
+| Public Behavior | Vaccine Acceptance | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_wcovid_vaccinated_appointment_or_accept` |
+| Public Behavior | COVID Symptom Searches on Google | [`google-symptoms`](covidcast-signals/google-symptoms.md) | `sum_anosmia_ageusia_smoothed_search` |
+| Early Indicators | COVID-Like Symptoms | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_wcli` |
+| Early Indicators | COVID-Like Symptoms in Community | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_whh_cmnty_cli` |
+| Early Indicators | COVID-Related Doctor Visits | [`doctor-visits`](covidcast-signals/doctor-visits.md) | `smoothed_adj_cli` |
+| Cases and Testing | COVID Cases | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `confirmed_7dav_incidence_prop` |
+| Late Indicators | COVID Hospital Admissions | [`hhs`](covidcast-signals/hhs.md) | `confirmed_admissions_covid_1d_prop_7dav` |
+| Late Indicators | Deaths | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `deaths_7dav_incidence_prop` |
+
+### All Available Sources and Signals
+
+Beyond the signals available on the COVIDcast dashboard, numerous other  signals are
+available through our [data export tool](https://delphi.cmu.edu/covidcast/export/) or directly through the API.
 
 ## Constructing API Queries
 

diff --git a/docs/api/covidcast_changelog.md b/docs/api/covidcast_changelog.md
@@ -1,7 +1,7 @@
 ---
 title: Signal Changelog
 parent: COVIDcast Main Endpoint
-nav_order: 3
+nav_order: 8
 ---
 
 # COVIDcast Signal Changelog
@@ -17,6 +17,8 @@ we **strongly recommend** that anyone using the API to download data regularly
 should subscribe to this list. We will only use the list to announce API
 changes, data corrections, and other information relevant to API users.
 
+For current information on how up-to-date our public health and behavior data is, how much of the country is covered by our public health and behavior data, and the data versioning effects present in our public health and behavior data, please see Delphi's [Indicator Status Overview page](https://delphi.cmu.edu/covidcast/indicator-status/).
+
 ## Table of contents
 {: .no_toc .text-delta}
 

diff --git a/docs/api/covidcast_clients.md b/docs/api/covidcast_clients.md
@@ -1,5 +1,5 @@
 ---
-title: API Clients
+title: COVIDcast API Clients
 parent: COVIDcast Main Endpoint
 nav_order: 1
 ---

diff --git a/docs/api/covidcast_geography.md b/docs/api/covidcast_geography.md
@@ -1,7 +1,7 @@
 ---
 title: Geographic Coding
 parent: COVIDcast Main Endpoint
-nav_order: 4
+nav_order: 5
 ---
 
 # COVIDcast Geographic Coding

diff --git a/docs/api/covidcast_meta.md b/docs/api/covidcast_meta.md
@@ -1,7 +1,7 @@
 ---
 title: Metadata
 parent: COVIDcast Main Endpoint
-nav_order: 6
+nav_order: 4
 ---
 
 # COVIDcast Metadata

diff --git a/docs/api/covidcast_signals.md b/docs/api/covidcast_signals.md
@@ -1,46 +1,7 @@
 ---
 title: Data Sources and Signals
 parent: COVIDcast Main Endpoint
-nav_order: 2
+nav_order: 3
 has_children: true
----
-
-# Delphi's COVID-19 Data Sources and Signals
-
-Delphi's COVID-19 Surveillance Streams data includes the following data sources.
-Data from most of these sources is typically updated daily. You can use the
-[`covidcast_meta`](covidcast_meta.md) endpoint to get summary information
-about the ranges of the different attributes for the different data sources.
-
-The API for retrieving data from these sources is described in the
-[COVIDcast endpoint documentation](covidcast.md). Changes and corrections to
-data from this endpoint are listed in the [changelog](covidcast_changelog.md).
-
-To obtain many of these signals and update them daily, Delphi has written
-extensive software to obtain data from various sources, aggregate the data,
-calculate statistical estimates, and format the data to be shared through the
-COVIDcast endpoint of the Delphi Epidata API. This code is 
-[open source and available on GitHub](https://github.com/cmu-delphi/covidcast-indicators),
-and contributions are welcome.
 
-## COVIDcast Dashboard Signals
-
-The following signals are currently displayed on [the public COVIDcast
-dashboard](https://delphi.cmu.edu/covidcast/):
-
-| Kind | Name | Source | Signal |
-|---|---|---|---|
-| Public Behavior | People Wearing Masks | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_wwearing_mask_7d` |
-| Public Behavior | Vaccine Acceptance | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_wcovid_vaccinated_appointment_or_accept` |
-| Public Behavior | COVID Symptom Searches on Google | [`google-symptoms`](covidcast-signals/google-symptoms.md) | `sum_anosmia_ageusia_smoothed_search` |
-| Early Indicators | COVID-Like Symptoms | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_wcli` |
-| Early Indicators | COVID-Like Symptoms in Community | [`fb-survey`](covidcast-signals/fb-survey.md) | `smoothed_whh_cmnty_cli` |
-| Early Indicators | COVID-Related Doctor Visits | [`doctor-visits`](covidcast-signals/doctor-visits.md) | `smoothed_adj_cli` |
-| Cases and Testing | COVID Cases | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `confirmed_7dav_incidence_prop` |
-| Late Indicators | COVID Hospital Admissions | [`hhs`](covidcast-signals/hhs.md) | `confirmed_admissions_covid_1d_prop_7dav` |
-| Late Indicators | Deaths | [`jhu-csse`](covidcast-signals/jhu-csse.md) | `deaths_7dav_incidence_prop` |
-
-## All Available Sources and Signals
-
-Beyond the signals available on the COVIDcast dashboard, numerous other signals are
-available through our [data export tool](https://delphi.cmu.edu/covidcast/export/) or directly through the API:
+---
diff --git a/docs/api/covidcast_times.md b/docs/api/covidcast_times.md
@@ -1,7 +1,7 @@
 ---
 title: Date Coding and Revisions
 parent: COVIDcast Main Endpoint
-nav_order: 5
+nav_order: 6
 ---
 
 # Date Coding and Revisions

diff --git a/docs/api/delphi.md b/docs/api/delphi.md
@@ -1,6 +1,6 @@
 ---
 title: Delphi Forecasts
-parent: Other Endpoints (COVID-19 and Other Diseases)
+parent: Other Endpoints
 ---
 
 # Delphi Forecasts