diff --git a/docs/about_delphi.md b/docs/about_delphi.md new file mode 100644 index 000000000..835d42c13 --- /dev/null +++ b/docs/about_delphi.md @@ -0,0 +1,15 @@ +--- +title: About Delphi +nav_order: 60 +has_children: false +--- + +# About The Delphi Group + +The Delphi Group's mission is to develop the theory and practice of epidemic detection, tracking and forecasting, and their use in decision making, both public and private. + +Our vision is to make this technology as useful as weather forecasting is today. + +Find out more about the Delphi Research Group on our offical webpage. +Please read our blog for additional news, findings, and musings from the team. + diff --git a/docs/api/README.md b/docs/api/README.md index a3a3986fa..6f38d8cf6 100644 --- a/docs/api/README.md +++ b/docs/api/README.md @@ -1,7 +1,7 @@ --- title: Other Endpoints (COVID-19 and Other Diseases) -nav_order: 3 has_children: true +nav_order: 3 --- # Other Endpoints (COVID-19 and Other Diseases) @@ -208,4 +208,4 @@ To access our Epidata API, visit our [Epidata API Client Libraries)](client_libr # Related Work -Please visit our [related works](related_work.md) page for more information. +Please visit our [related works](../related_work.md) page for more information. diff --git a/docs/api/api_keys.md b/docs/api/api_keys.md index 21e875fe4..d8c5ab306 100644 --- 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 index 25295e512..29ae7ebe8 100644 --- a/docs/api/cdc.md +++ b/docs/api/cdc.md @@ -1,6 +1,8 @@ --- -title: CDC -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive CDC +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # CDC diff --git a/docs/api/client_libraries.md b/docs/api/client_libraries.md index 64116b150..cf27e30ca 100644 --- a/docs/api/client_libraries.md +++ b/docs/api/client_libraries.md @@ -1,10 +1,10 @@ --- -title: Epidata API Client Libraries +title: API Clients parent: Other Endpoints (COVID-19 and Other Diseases) nav_order: 1 --- -# Epidata API Client Libraries +# Epidata API Clients To access Delphi Epidata programmatically, we recommend our client libraries: @@ -12,7 +12,7 @@ To access Delphi Epidata programmatically, we recommend our client libraries: - Python: [delphi-epidata](https://pypi.org/project/delphi-epidata/) (soon to be replaced with [epidatpy](https://github.com/cmu-delphi/epidatpy)), - Javascript: [delphi-epidata](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js). -For anyone looking for COVIDCast data, please visit our [COVIDCast Libraries](covidcast_clients.md). +For anyone looking for COVIDCast data, please visit our [COVIDCast API Client Libraries](covidcast_clients.md). The following samples show how to import the library and fetch Delphi's COVID-19 Surveillance Streams from Facebook Survey CLI for county 06001 and days diff --git a/docs/api/covid_hosp.md b/docs/api/covid_hosp.md index d61c6eebf..30d56e351 100644 --- a/docs/api/covid_hosp.md +++ b/docs/api/covid_hosp.md @@ -1,6 +1,8 @@ --- -title: COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # COVID-19 Hospitalization by State diff --git a/docs/api/covid_hosp_facility.md b/docs/api/covid_hosp_facility.md index fe24bb0e6..3cca8b20a 100644 --- a/docs/api/covid_hosp_facility.md +++ b/docs/api/covid_hosp_facility.md @@ -1,6 +1,8 @@ --- -title: COVID-19 Reported Patient Impact and Hospital Capacity by Facility -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive COVID-19 Reported Patient Impact and Hospital Capacity by Facility +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # COVID-19 Hospitalization by Facility diff --git a/docs/api/covid_hosp_facility_lookup.md b/docs/api/covid_hosp_facility_lookup.md index 25e97c956..98356d0cd 100644 --- a/docs/api/covid_hosp_facility_lookup.md +++ b/docs/api/covid_hosp_facility_lookup.md @@ -1,6 +1,8 @@ --- -title: COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # COVID-19 Hospitalization: Facility Lookup diff --git a/docs/api/covidcast-signals/_source-template.md b/docs/api/covidcast-signals/_source-template.md index 137d7f38a..f2e966817 100644 --- a/docs/api/covidcast-signals/_source-template.md +++ b/docs/api/covidcast-signals/_source-template.md @@ -1,7 +1,7 @@ --- title: SOURCE NAME parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +grand_parent: Main Endpoint (COVIDcast) --- # SOURCE NAME diff --git a/docs/api/covidcast-signals/chng.md b/docs/api/covidcast-signals/chng.md index 1a9ebafd0..06b6d5a29 100644 --- a/docs/api/covidcast-signals/chng.md +++ b/docs/api/covidcast-signals/chng.md @@ -1,7 +1,8 @@ --- title: Change Healthcare parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +grand_parent: Main Endpoint (COVIDcast) +nav_order: 1 --- # Change Healthcare diff --git a/docs/api/covidcast-signals/covid-act-now.md b/docs/api/covidcast-signals/covid-act-now.md index 670bda61f..204f14685 100644 --- a/docs/api/covidcast-signals/covid-act-now.md +++ b/docs/api/covidcast-signals/covid-act-now.md @@ -1,7 +1,8 @@ --- -title: COVID Act Now -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive COVID Act Now +parent: Data Sources and Signals +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # COVID Act Now (CAN) diff --git a/docs/api/covidcast-signals/doctor-visits.md b/docs/api/covidcast-signals/doctor-visits.md index 036a98de0..5eb9c96a9 100644 --- a/docs/api/covidcast-signals/doctor-visits.md +++ b/docs/api/covidcast-signals/doctor-visits.md @@ -1,7 +1,8 @@ --- title: Doctor Visits parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +grand_parent: Main Endpoint (COVIDcast) +nav_order: 1 --- # Doctor Visits diff --git a/docs/api/covidcast-signals/dsew-cpr.md b/docs/api/covidcast-signals/dsew-cpr.md index d187e10b3..9a0050924 100644 --- a/docs/api/covidcast-signals/dsew-cpr.md +++ b/docs/api/covidcast-signals/dsew-cpr.md @@ -1,7 +1,8 @@ --- -title: Data Strategy and Execution Workgroup Community Profile Report -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive Data Strategy and Execution Workgroup Community Profile Report +parent: Data Sources and Signals +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # Data Strategy and Execution Workgroup Community Profile Report (CPR) diff --git a/docs/api/covidcast-signals/fb-survey.md b/docs/api/covidcast-signals/fb-survey.md index fee18715b..6b798ec7a 100644 --- a/docs/api/covidcast-signals/fb-survey.md +++ b/docs/api/covidcast-signals/fb-survey.md @@ -1,10 +1,11 @@ --- -title: COVID-19 Trends and Impact Survey -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive COVID-19 Trends and Impact Survey +parent: Data Sources and Signals +grand_parent: Main Endpoint (COVIDcast) +nav_order: 2 --- -# COVID-19 Trends and Impact Survey +# COVID-19 Trends and Impact Survey 2020-2022 (Facebook Survey) {: .no_toc} * **Source name:** `fb-survey` diff --git a/docs/api/covidcast-signals/ght.md b/docs/api/covidcast-signals/ght.md index 241c14bf7..d479b9932 100644 --- a/docs/api/covidcast-signals/ght.md +++ b/docs/api/covidcast-signals/ght.md @@ -1,7 +1,8 @@ --- title: Google Health Trends parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # Google Health Trends diff --git a/docs/api/covidcast-signals/google-survey.md b/docs/api/covidcast-signals/google-survey.md index bdc3a5654..c1f4819ab 100644 --- a/docs/api/covidcast-signals/google-survey.md +++ b/docs/api/covidcast-signals/google-survey.md @@ -1,7 +1,8 @@ --- -title: Google Symptom Surveys -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive Google Symptom Surveys +parent: Data Sources and Signals +grand_parent: Main Endpoint (COVIDcast) +nav_order: 2 --- # Google Symptom Surveys @@ -25,7 +26,7 @@ is sick (fever, along with cough, or shortness of breath, or difficulty breathing) right now?" Using this survey data, we estimate the percentage of people in a given location, on a given day, that *know somebody who has a COVID-like illness*. This estimates a similar quantity to the `*_cmnty_cli` -signals from the [Symptom Surveys](fb-survey.md) (`fb-survey`) source, but using +signals from the [COVID-19 Trends and Impact Survey](fb-survey.md) (`fb-survey`) source, but using a different survey population and recruitment method. The survey sampled from all counties with greater than 100,000 population, along @@ -263,12 +264,12 @@ probabilities and contribute variance. ### Smoothing -Additionally, as with the Facebook surveys, we consider estimates formed by +Additionally, as with the COVID-19 Trends and Impact Survey, we consider estimates formed by pooling data over time. That is, daily, for each location, we first pool all data available in that location over the last 5 days, and compute the estimates given above using all five days of data. -In contrast to the Facebook surveys, this pooling does not significantly change +In contrast to the COVID-19 Trends and Impact Survey, this pooling does not significantly change the availability of estimates, because of our stratified sampling procedure (essentially always) delivers sufficient data at the county level---at least 100 survey responses---to warrant their own estimates. However, the pooling diff --git a/docs/api/covidcast-signals/google-symptoms.md b/docs/api/covidcast-signals/google-symptoms.md index 11d53d910..b75c7d5b7 100644 --- a/docs/api/covidcast-signals/google-symptoms.md +++ b/docs/api/covidcast-signals/google-symptoms.md @@ -1,7 +1,8 @@ --- -title: Google Search Trends symptoms dataset +title: inactive Google Search Trends Symptoms parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # Google Symptoms diff --git a/docs/api/covidcast-signals/hhs.md b/docs/api/covidcast-signals/hhs.md index a77187532..7dd2d9d04 100644 --- a/docs/api/covidcast-signals/hhs.md +++ b/docs/api/covidcast-signals/hhs.md @@ -1,7 +1,8 @@ --- -title: Department of Health & Human Services -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive Department of Health & Human Services +parent: Data Sources and Signals +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # Department of Health & Human Services diff --git a/docs/api/covidcast-signals/hospital-admissions.md b/docs/api/covidcast-signals/hospital-admissions.md index c988b95e8..1dcd5959f 100644 --- a/docs/api/covidcast-signals/hospital-admissions.md +++ b/docs/api/covidcast-signals/hospital-admissions.md @@ -1,7 +1,8 @@ --- title: Hospital Admissions parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +grand_parent: Main Endpoint (COVIDcast) +nav_order: 1 --- # Hospital Admissions diff --git a/docs/api/covidcast-signals/indicator-combination.md b/docs/api/covidcast-signals/indicator-combination.md index 54c5a3b78..289d0a353 100644 --- a/docs/api/covidcast-signals/indicator-combination.md +++ b/docs/api/covidcast-signals/indicator-combination.md @@ -1,7 +1,8 @@ --- -title: Indicator Combination -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive Indicator Combination +parent: Data Sources and Signals +grand_parent: Main Endpoint (COVIDcast) +nav_order: 2 --- # Indicator Combination diff --git a/docs/api/covidcast-signals/jhu-csse.md b/docs/api/covidcast-signals/jhu-csse.md index 44955430c..03e0544bd 100644 --- a/docs/api/covidcast-signals/jhu-csse.md +++ b/docs/api/covidcast-signals/jhu-csse.md @@ -1,7 +1,8 @@ --- -title: JHU Cases and Deaths -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive JHU Cases and Deaths +parent: Data Sources and Signals +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # JHU Cases and Deaths diff --git a/docs/api/covidcast-signals/nchs-mortality.md b/docs/api/covidcast-signals/nchs-mortality.md index 9e46aa4d4..278061c04 100644 --- a/docs/api/covidcast-signals/nchs-mortality.md +++ b/docs/api/covidcast-signals/nchs-mortality.md @@ -1,7 +1,8 @@ --- title: NCHS Mortality Data parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +grand_parent: Main Endpoint (COVIDcast) +nav_order: 1 --- # NCHS Mortality Data diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 3b171d5dd..6536bac8c 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -1,7 +1,8 @@ --- title: NSSP ED Visits parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +grand_parent: Main Endpoint (COVIDcast) +nav_order: 1 --- # National Syndromic Surveillance Program Emergency Department Visits {: .no_toc} diff --git a/docs/api/covidcast-signals/quidel-flu.md b/docs/api/covidcast-signals/quidel-flu.md deleted file mode 100644 index 1c7583845..000000000 --- a/docs/api/covidcast-signals/quidel-flu.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -title: Quidel -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint ---- - -# Quidel -{: .no_toc} - -* **Source name:** `quidel` - -## Table of Contents -{: .no_toc .text-delta} - -1. TOC -{:toc} - -## Accessibility: Delphi-internal only - -## COVID-19 Tests -These signals are still active. Documentation is available on the [Quidel page](quidel.md). - -## Flu Tests - -* **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)) - -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. The data may be updated again when the Winter 2020 flu season begins. - -| Signal | Description | -| --- | --- | -| `raw_pct_negative` | The percentage of flu tests that are negative, suggesting the patient's illness has another cause, possibly COVID-19
**Earliest date available:** 2020-01-31 | -| `smoothed_pct_negative` | Same as above, but smoothed in time
**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
**Earliest date available:** 2020-01-31 | -| `smoothed_tests_per_device` | Same as above, but smoothed in time
**Earliest date available:** 2020-01-31 | diff --git a/docs/api/covidcast-signals/quidel.md b/docs/api/covidcast-signals/quidel.md index 0072769ef..430339291 100644 --- a/docs/api/covidcast-signals/quidel.md +++ b/docs/api/covidcast-signals/quidel.md @@ -1,14 +1,13 @@ --- title: Quidel parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint +grand_parent: Main Endpoint (COVIDcast) +nav_order: 1 --- # Quidel {: .no_toc} -* **Source name:** `quidel` - ## Table of Contents {: .no_toc .text-delta} @@ -17,15 +16,18 @@ grand_parent: COVIDcast Main Endpoint ## Accessibility: Delphi-internal only -## COVID-19 Tests +## Quidel COVID-19 Tests -* **Earliest issue available:** July 29, 2020 +* **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 +161,39 @@ 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). \ No newline at end of file +## 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
**Earliest date available:** 2020-01-31 | +| `smoothed_pct_negative` | Same as above, but smoothed in time
**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
**Earliest date available:** 2020-01-31 | +| `smoothed_tests_per_device` | Same as above, but smoothed in time
**Earliest date available:** 2020-01-31 | diff --git a/docs/api/covidcast-signals/safegraph.md b/docs/api/covidcast-signals/safegraph.md index 4e8c0091b..776dd98ed 100644 --- a/docs/api/covidcast-signals/safegraph.md +++ b/docs/api/covidcast-signals/safegraph.md @@ -1,7 +1,8 @@ --- -title: SafeGraph -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive SafeGraph +parent: Data Sources and Signals +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # SafeGraph diff --git a/docs/api/covidcast-signals/usa-facts.md b/docs/api/covidcast-signals/usa-facts.md index e0160cfde..5fc67ec1f 100644 --- a/docs/api/covidcast-signals/usa-facts.md +++ b/docs/api/covidcast-signals/usa-facts.md @@ -1,7 +1,8 @@ --- -title: USAFacts Cases and Deaths -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive USAFacts Cases and Deaths +parent: Data Sources and Signals +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- # USAFacts Cases and Deaths diff --git a/docs/api/covidcast-signals/youtube-survey.md b/docs/api/covidcast-signals/youtube-survey.md index 9b7105171..dcbc7b879 100644 --- a/docs/api/covidcast-signals/youtube-survey.md +++ b/docs/api/covidcast-signals/youtube-survey.md @@ -1,7 +1,8 @@ --- -title: Youtube Survey -parent: Inactive Signals -grand_parent: COVIDcast Main Endpoint +title: inactive Youtube Survey +parent: Data Sources and Signals +nav_order: 2 +grand_parent: Main Endpoint (COVIDcast) --- [//]: # (code at https://github.com/cmu-delphi/covid-19/tree/deeb4dc1e9a30622b415361ef6b99198e77d2a94/youtube) diff --git a/docs/api/covidcast.md b/docs/api/covidcast.md index bf931fe4c..94fb9acb8 100644 --- a/docs/api/covidcast.md +++ b/docs/api/covidcast.md @@ -1,10 +1,12 @@ --- -title: COVIDcast Main Endpoint +title: Main Endpoint (COVIDcast) has_children: true nav_order: 2 --- -# COVIDcast Epidata API +# Main Epidata API + +This endpoint was previously known as COVIDcast. This is the documentation for accessing Delphi's COVID-19 indicators via the `covidcast` endpoint of [Delphi](https://delphi.cmu.edu/)'s epidemiological data API. This API provides data on the spread and impact of the COVID-19 pandemic across the United States, most of which is available at the @@ -86,8 +88,43 @@ 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 index bd7313ea2..f1efed34e 100644 --- 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 +parent: Main Endpoint (COVIDcast) +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 index c85389f5f..8066e33f5 100644 --- a/docs/api/covidcast_clients.md +++ b/docs/api/covidcast_clients.md @@ -1,15 +1,15 @@ --- title: API Clients -parent: COVIDcast Main Endpoint +parent: Main Endpoint (COVIDcast) nav_order: 1 --- -# COVIDcast Libraries +# Main Endpoint API Clients To access COVIDcast data, we recommend using the following client libraries: -- R: [epidatr](https://cmu-delphi.github.io/epidatr/), -- Python: [covidcast](https://cmu-delphi.github.io/covidcast/covidcast-py/html/) (soon to be replaced with [epidatpy](https://github.com/cmu-delphi/epidatpy)). +- R: [epidatr](https://cmu-delphi.github.io/epidatr/) +- Python: [covidcast](https://cmu-delphi.github.io/covidcast/covidcast-py/html/) (soon to be replaced with [epidatpy](https://github.com/cmu-delphi/epidatpy)) These packages provide a convenient way to obtain COVIDcast data as a data frame ready to be used in further analyses and provide convenient mapping and analysis diff --git a/docs/api/covidcast_geography.md b/docs/api/covidcast_geography.md index 365817a69..a88b17cd3 100644 --- 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 +parent: Main Endpoint (COVIDcast) +nav_order: 5 --- # COVIDcast Geographic Coding diff --git a/docs/api/covidcast_inactive_signals.md b/docs/api/covidcast_inactive_signals.md deleted file mode 100644 index 880f47d8a..000000000 --- a/docs/api/covidcast_inactive_signals.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -title: Inactive Signals -parent: COVIDcast Main Endpoint -has_children: true -nav_order: 7 ---- - -# COVIDcast Inactive Signals - -These signals are currently not updated because the sources have become unavailable, other sources have replaced them, or additional work is required for us to continue updating them. Some of these sources may return in the coming months. diff --git a/docs/api/covidcast_licensing.md b/docs/api/covidcast_licensing.md index bcdc2a334..d6efaf62c 100644 --- a/docs/api/covidcast_licensing.md +++ b/docs/api/covidcast_licensing.md @@ -1,12 +1,12 @@ --- -title: COVIDcast Data Licensing -parent: COVIDcast Main Endpoint +title: Data Licensing +parent: Main Endpoint (COVIDcast) nav_order: 2 --- -# Licensing for Delphi's COVID-19 Data Streams +# Licensing for the Main Endpoint -When you use data from Delphi's COVIDcast Epidata API, we ask that you attribute +When you use data from Delphi's Epidata API, we ask that you attribute the source and follow the terms of the data's licensing agreement. The API contains some data streams produced internally by Delphi, which should be attributed to Delphi, and some republished from other sources, which should be diff --git a/docs/api/covidcast_meta.md b/docs/api/covidcast_meta.md index 08c3990c8..fb5221579 100644 --- a/docs/api/covidcast_meta.md +++ b/docs/api/covidcast_meta.md @@ -1,7 +1,8 @@ --- title: Metadata -parent: COVIDcast Main Endpoint -nav_order: 6 +parent: Data Sources and Signals +grand_parent: Main Endpoint (COVIDcast) +nav_order: 0 --- # COVIDcast Metadata diff --git a/docs/api/covidcast_signals.md b/docs/api/covidcast_signals.md index 4e69b6d73..1f5ce38b6 100644 --- a/docs/api/covidcast_signals.md +++ b/docs/api/covidcast_signals.md @@ -1,10 +1,10 @@ --- title: Data Sources and Signals -parent: COVIDcast Main Endpoint -nav_order: 2 +parent: Main Endpoint (COVIDcast) +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. @@ -43,4 +43,4 @@ dashboard](https://delphi.cmu.edu/covidcast/): ## 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: +available through our [data export tool](https://delphi.cmu.edu/covidcast/export/) or directly through the API: \ No newline at end of file diff --git a/docs/api/covidcast_times.md b/docs/api/covidcast_times.md index 2e2680a76..0eace1551 100644 --- 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 +parent: Main Endpoint (COVIDcast) +nav_order: 6 --- # Date Coding and Revisions diff --git a/docs/api/delphi.md b/docs/api/delphi.md index 1cc645b0a..dae9c672b 100644 --- a/docs/api/delphi.md +++ b/docs/api/delphi.md @@ -1,6 +1,8 @@ --- -title: Delphi Forecasts -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Delphi Forecasts +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Delphi Forecasts diff --git a/docs/api/delphi_research_group.md b/docs/api/delphi_research_group.md new file mode 100644 index 000000000..8c0c2d93a --- /dev/null +++ b/docs/api/delphi_research_group.md @@ -0,0 +1 @@ +https://delphi.cmu.edu/ \ No newline at end of file diff --git a/docs/api/dengue_nowcast.md b/docs/api/dengue_nowcast.md index abaf15c08..52dc80fca 100644 --- a/docs/api/dengue_nowcast.md +++ b/docs/api/dengue_nowcast.md @@ -1,6 +1,8 @@ --- -title: Dengue Nowcast -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Dengue Nowcast +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Delphi's Dengue Nowcast diff --git a/docs/api/dengue_sensors.md b/docs/api/dengue_sensors.md index 470861bbf..7c86a1688 100644 --- a/docs/api/dengue_sensors.md +++ b/docs/api/dengue_sensors.md @@ -1,6 +1,8 @@ --- -title: Dengue Digital Surveillance -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Dengue Digital Surveillance +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Dengue Digital Surveillance Sensors diff --git a/docs/api/ecdc_ili.md b/docs/api/ecdc_ili.md index 399f7f015..c379fe369 100644 --- a/docs/api/ecdc_ili.md +++ b/docs/api/ecdc_ili.md @@ -1,6 +1,8 @@ --- -title: ECDC ILI -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive ECDC ILI +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # ECDC ILI diff --git a/docs/api/epidata_signals.md b/docs/api/epidata_signals.md new file mode 100644 index 000000000..52415109e --- /dev/null +++ b/docs/api/epidata_signals.md @@ -0,0 +1,23 @@ +--- +title: Data Sources and Signals +parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 +has_children: true + +--- + +# Delphi's Epidata Data Sources and Signals + +Delphi's Epidata endpoints include the following data sources. +Most of these sources are updated weekly. +Unlike [the main endpoint](covidcast.md), the format of different Epidata endpoints varies. +The API for retrieving data from these sources is described in the +[API clients documentation](client_libraries.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 Delphi Epidata API. +This code is +[open source and available on GitHub](https://github.com/cmu-delphi/delphi-epidata), +and contributions are welcome. + diff --git a/docs/api/flusurv.md b/docs/api/flusurv.md index b33f5c22d..d7f017883 100644 --- a/docs/api/flusurv.md +++ b/docs/api/flusurv.md @@ -1,6 +1,8 @@ --- -title: Flusurv -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Flusurv +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # FluSurv diff --git a/docs/api/fluview.md b/docs/api/fluview.md index 8bf4a25ef..34d878cd7 100644 --- a/docs/api/fluview.md +++ b/docs/api/fluview.md @@ -1,6 +1,8 @@ --- title: FluView -parent: Other Endpoints (COVID-19 and Other Diseases) +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 1 --- # FluView diff --git a/docs/api/fluview_clinical.md b/docs/api/fluview_clinical.md index d5fd12db2..ca2b7b801 100644 --- a/docs/api/fluview_clinical.md +++ b/docs/api/fluview_clinical.md @@ -1,6 +1,8 @@ --- title: FluView Clinical -parent: Other Endpoints (COVID-19 and Other Diseases) +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 1 --- # FluView Clinical diff --git a/docs/api/fluview_meta.md b/docs/api/fluview_meta.md index c3fbb25b4..e12d1f25d 100644 --- a/docs/api/fluview_meta.md +++ b/docs/api/fluview_meta.md @@ -1,6 +1,8 @@ --- title: FluView metadata -parent: Other Endpoints (COVID-19 and Other Diseases) +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 1 --- # FluView metadata diff --git a/docs/api/gft.md b/docs/api/gft.md index 72898cb9b..c2642269b 100644 --- a/docs/api/gft.md +++ b/docs/api/gft.md @@ -1,6 +1,8 @@ --- -title: Google Flu Trends -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Google Flu Trends +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Google Flu Trends diff --git a/docs/api/ght.md b/docs/api/ght.md index 107d5b10e..67f23f435 100644 --- a/docs/api/ght.md +++ b/docs/api/ght.md @@ -1,6 +1,8 @@ --- -title: Google Health Trends -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Google Health Trends +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Google Health Trends diff --git a/docs/api/kcdc_ili.md b/docs/api/kcdc_ili.md index b516ce04e..340d886d2 100644 --- a/docs/api/kcdc_ili.md +++ b/docs/api/kcdc_ili.md @@ -1,6 +1,8 @@ --- -title: KCDC ILI -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive KCDC ILI +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # KCDC ILI diff --git a/docs/api/meta.md b/docs/api/meta.md index bccd7c0fd..752e85fcb 100644 --- a/docs/api/meta.md +++ b/docs/api/meta.md @@ -1,6 +1,8 @@ --- -title: Metadata -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Metadata +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # API Metadata diff --git a/docs/api/meta_norostat.md b/docs/api/meta_norostat.md index 217b20fbf..1f2754eea 100644 --- a/docs/api/meta_norostat.md +++ b/docs/api/meta_norostat.md @@ -1,6 +1,8 @@ --- -title: NoroSTAT Metadata -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive NoroSTAT Metadata +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # NoroSTAT Metadata diff --git a/docs/api/missing_codes.md b/docs/api/missing_codes.md index d49bdbd98..30a1ee4cd 100644 --- a/docs/api/missing_codes.md +++ b/docs/api/missing_codes.md @@ -1,7 +1,7 @@ --- title: NaN Missing Codes -parent: COVIDcast Main Endpoint -nav_order: 5 +parent: Main Endpoint (COVIDcast) +nav_order: 7 --- # Missing Value Coding diff --git a/docs/api/nidss_dengue.md b/docs/api/nidss_dengue.md index ab7349658..fd97a7c08 100644 --- a/docs/api/nidss_dengue.md +++ b/docs/api/nidss_dengue.md @@ -1,6 +1,8 @@ --- -title: NIDSS Dengue -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive NIDSS Dengue +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # NIDSS Dengue diff --git a/docs/api/nidss_flu.md b/docs/api/nidss_flu.md index 4af0d61d6..d168bcf82 100644 --- a/docs/api/nidss_flu.md +++ b/docs/api/nidss_flu.md @@ -1,6 +1,8 @@ --- -title: NIDSS Flu -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive NIDSS Flu +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # NIDSS Flu diff --git a/docs/api/norostat.md b/docs/api/norostat.md index dded4ec13..80c289c84 100644 --- a/docs/api/norostat.md +++ b/docs/api/norostat.md @@ -1,6 +1,8 @@ --- -title: NoroSTAT -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive NoroSTAT +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # NoroSTAT diff --git a/docs/api/nowcast.md b/docs/api/nowcast.md index 988c83810..aa82077a0 100644 --- a/docs/api/nowcast.md +++ b/docs/api/nowcast.md @@ -1,6 +1,8 @@ --- -title: ILI Nearby Nowcast -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive ILI Nearby Nowcast +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # ILI Nearby Nowcast diff --git a/docs/api/paho_dengue.md b/docs/api/paho_dengue.md index 46e1706c2..70d3bb300 100644 --- a/docs/api/paho_dengue.md +++ b/docs/api/paho_dengue.md @@ -1,6 +1,8 @@ --- -title: PAHO Dengue -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive PAHO Dengue +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # PAHO Dengue diff --git a/docs/api/privacy_statement.md b/docs/api/privacy_statement.md index eccaec14d..1b3108a49 100644 --- a/docs/api/privacy_statement.md +++ b/docs/api/privacy_statement.md @@ -1,12 +1,12 @@ --- title: Privacy Statement -parent: API Keys +parent: Epidata API Intro +nav_order: 3 --- -# Delphi Privacy Statement +# Privacy Statement -Anyone may access the Epidata API anonymously without providing any personal -data. +Anyone may access the Epidata API anonymously without providing any personal data. For anyone looking for COVIDCast data licensing, please visit our [COVIDCast Data Licensing](covidcast_licensing.md). Some features of the API are only available by registering for an API key. We require an email address for all registrations so that we can contact you to diff --git a/docs/api/quidel.md b/docs/api/quidel.md index 0abb412ca..28655e219 100644 --- a/docs/api/quidel.md +++ b/docs/api/quidel.md @@ -1,29 +1,25 @@ --- -title: Quidel -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Quidel +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Quidel -This is the documentation of the API for accessing the Quidel (`quidel`) endpoint of -the [Delphi](https://delphi.cmu.edu/)'s epidemiological data. +This is the documentation of the API for accessing the Quidel (`quidel`) endpoint of the Delphi’s epidemiological data. -General topics not specific to any particular endpoint are discussed in the -[API overview](README.md). Such topics include: -[contributing](README.md#contributing), [citing](README.md#citing), and -[data licensing](README.md#data-licensing). +General topics not specific to any particular endpoint are discussed in the [API overview](https://cmu-delphi.github.io/delphi-epidata/). Such topics include: [contributing](https://cmu-delphi.github.io/delphi-epidata/api/README.html#contributing), [citing](https://cmu-delphi.github.io/delphi-epidata/api/README.html#citing), and [data licensing](https://cmu-delphi.github.io/delphi-epidata/api/README.html#data-licensing). ## Quidel Data Data provided by Quidel Corp., which contains flu lab test results. -... - -# The API +## The API The base URL is: https://api.delphi.cmu.edu/epidata/quidel/ -See [this documentation](README.md) for details on specifying epiweeks, dates, and lists. +See this [documentation](https://cmu-delphi.github.io/delphi-epidata/api/README.html) for details on specifying epiweeks, dates, and lists. ## Parameters @@ -42,12 +38,4 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a | `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer | | `epidata` | list of results | array of objects | | ... | ... | ... | -| `message` | `success` or error message | string | - -# Example URLs - - - -# Code Samples - - +| `message` | `success` or error message | string | \ No newline at end of file diff --git a/docs/api/sensors.md b/docs/api/sensors.md index c4430e1f1..0a2238ca5 100644 --- a/docs/api/sensors.md +++ b/docs/api/sensors.md @@ -1,6 +1,8 @@ --- -title: Digital Surveillance Sensors -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Digital Surveillance Sensors +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Digital Surveillance Sensors diff --git a/docs/api/twitter.md b/docs/api/twitter.md index dc2196f47..7a0cdec4b 100644 --- a/docs/api/twitter.md +++ b/docs/api/twitter.md @@ -1,6 +1,8 @@ --- -title: Twitter Stream -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Twitter Stream +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Twitter Stream diff --git a/docs/api/wiki.md b/docs/api/wiki.md index 136711f46..ba780ea6f 100644 --- a/docs/api/wiki.md +++ b/docs/api/wiki.md @@ -1,6 +1,8 @@ --- -title: Wikipedia Access -parent: Other Endpoints (COVID-19 and Other Diseases) +title: inactive Wikipedia Access +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 2 --- # Wikipedia Access diff --git a/docs/developer_support.md b/docs/developer_support.md new file mode 100644 index 000000000..ddba4ff89 --- /dev/null +++ b/docs/developer_support.md @@ -0,0 +1,8 @@ +--- +title: Developer Support +nav_order: 5 +has_children: true +--- + +# Developer Support +Delphi's Developer Support section provides several helpful resources for developers including a quickstart guide and tutorial. diff --git a/docs/epidata_development.md b/docs/epidata_development.md index eb38e6ae9..271c9c8c6 100644 --- a/docs/epidata_development.md +++ b/docs/epidata_development.md @@ -1,6 +1,7 @@ --- -title: Epidata API Development Guide -nav_order: 4 +title: Development Guide +parent: Developer Support +nav_order: 1 --- # Epidata API Development Guide @@ -177,3 +178,9 @@ The bare minimum to set up instrumentation is to supply the DSN for the [epidata - Once you have the DSN, add it to your local `.env` file and rebuild your containers to start sending telemetry to Sentry. Additional internal documentation for Sentry can be found [here](https://bookstack.delphi.cmu.edu/books/systems-handbook/page/sentry). + +## COVIDcast Development Guide + +For information on accessing Delphi's COVID-19 indicators via the `covidcast` endpoint of [Delphi](https://delphi.cmu.edu/)'s +epidemiological data API, please see [COVIDcast Epidata API](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html). This API provides data on the spread and impact of the COVID-19 pandemic across the United States, most of which is available at the +county level and updated daily. \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index 700fea3fc..bc301ebe0 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,7 @@ --- -title: Epidata API Home -nav_order: 0 +title: Epidata API Intro +has_children: true +nav_order: 1 --- # The Epidata API diff --git a/docs/new_endpoint_tutorial.md b/docs/new_endpoint_tutorial.md index abf8a5fa1..6149afa4e 100644 --- a/docs/new_endpoint_tutorial.md +++ b/docs/new_endpoint_tutorial.md @@ -1,9 +1,10 @@ --- -title: New Endpoint Tutorial -nav_order: 5 +title: "Adding a New API Endpoint" +parent: Developer Support +nav_order: 2 --- -# Tutorial: Adding a new API endpoint +# Adding a new API endpoint **Prerequisite:** this guide assumes that you have read the [epidata development guide](epidata_development.md). @@ -18,7 +19,7 @@ In this tutorial we'll create a brand new endpoint for the Epidata API: 5. update API documentation for the new endpoint 6. run all unit and integration tests -# setup +## Setup Follow [the backend guide](https://github.com/cmu-delphi/operations/blob/main/docs/backend_development.md) @@ -45,7 +46,7 @@ tree -L 3 .    └── undef-analysis ``` -# the data +## The data Here's the requirement: we need to quickly surface the most recent "issue" (epiweek of publication) for the existing [`fluview` endpoint](api/fluview.md). @@ -62,14 +63,14 @@ the following: - latest "issue", which is the publication epiweek - total size of the table -# update the server +## Update the server 1. create a new file in `/src/server/endpoints/` e.g., `fluview_meta.py`, or copy an existing one. 2. edit the created file `Blueprint("fluview_meta", __name__)` such that the first argument matches the target endpoint name 3. edit the existing `/src/server/endpoints/__init__.py` to add the newly-created file to the imports (top) and to the list of endpoints (below). -# update the client libraries +## Update the client libraries There are currently four client libraries. They all need to be updated to make the new `fluview_meta` endpoint available to callers. The pattern is very @@ -151,7 +152,7 @@ Here's what we add to each client: fluview_meta = fluview_meta, ``` -# add an integration test +## Add an integration test Now that we've changed several files, we need to make sure that the changes work as intended _before_ submitting code for review or committing code to the @@ -204,7 +205,7 @@ def test_round_trip(self): }) ``` -# write documentation +## Write documentation This consists of two steps: add a new document for the `fluview_meta` endpoint, and add a new entry to the existing table of endpoints. @@ -221,9 +222,9 @@ the following row in the appropriate place (i.e., next to the row for | [`fluview_meta`](fluview_meta.md) | FluView Metadata | Summary data about [`fluview`](fluview.md). | no | ``` -# run tests +## Run tests -## unit +### Unit Finally, we just need to run all new and existing tests. It is recommended to start with the unit tests because they are faster to build, run, and either @@ -259,15 +260,14 @@ and with pdb enabled like this: docker run -it --rm delphi_python pytest repos/delphi/delphi-epidata/tests/ --pdb ``` -## integration +### Integration Integration tests require more effort and take longer to set up and run. However, they allow us to test that various pieces are working together correctly. Many of these pieces we can't test individually with unit tests (e.g., database, and the API server), so integration tests are the only way we -can be confident that our changes won't break the API. Follow the [epidata -development guide](epidata_development.md#test). In summary, assuming you have -already built the `delphi_python` image above: +can be confident that our changes won't break the API. In summary, +assuming you have already built the `delphi_python` image above: ```bash # build web and database images for epidata @@ -314,7 +314,7 @@ and with pdb enabled like this: docker run --network delphi-net -it --rm delphi_python pytest repos/delphi/delphi-epidata/integrations/ --pdb ``` -# code review and submission +## Code review and submission All tests pass, and the changes are working as intended. Now submit the code for review, (e.g., by opening a pull request on GitHub). For an example, see the diff --git a/docs/related_work.md b/docs/related_work.md index 5f13a6ac0..15c4b726b 100644 --- a/docs/related_work.md +++ b/docs/related_work.md @@ -1,4 +1,10 @@ -# Related work +--- +title: Motivating Works +parent: Epidata API Intro +nav_order: 4 +--- + +# Motivating Works The works listed below, along with numerous others, were an early inspiration for the Epidata API: diff --git a/docs/symptom-survey/coding.md b/docs/symptom-survey/coding.md index c94d53c01..72deabb24 100644 --- a/docs/symptom-survey/coding.md +++ b/docs/symptom-survey/coding.md @@ -1,6 +1,6 @@ --- title: Questions and Coding -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 6 --- diff --git a/docs/symptom-survey/collaboration-revision.md b/docs/symptom-survey/collaboration-revision.md index e344f5ba9..6cc65e670 100644 --- a/docs/symptom-survey/collaboration-revision.md +++ b/docs/symptom-survey/collaboration-revision.md @@ -1,6 +1,6 @@ --- title: Collaboration and Survey Revision -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 1 --- diff --git a/docs/symptom-survey/contingency-tables.md b/docs/symptom-survey/contingency-tables.md index 832737c9e..a842a02cd 100644 --- a/docs/symptom-survey/contingency-tables.md +++ b/docs/symptom-survey/contingency-tables.md @@ -1,6 +1,6 @@ --- title: Contingency Tables -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 4 --- diff --git a/docs/symptom-survey/data-access.md b/docs/symptom-survey/data-access.md index 7cb49dfaf..23f76afcc 100644 --- a/docs/symptom-survey/data-access.md +++ b/docs/symptom-survey/data-access.md @@ -1,6 +1,6 @@ --- title: Getting Data Access -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 0 --- diff --git a/docs/symptom-survey/end-of-survey.md b/docs/symptom-survey/end-of-survey.md index 30d9fc597..f04cc55c6 100644 --- a/docs/symptom-survey/end-of-survey.md +++ b/docs/symptom-survey/end-of-survey.md @@ -1,6 +1,6 @@ --- title: End of CTIS Data Collection -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 11 --- diff --git a/docs/symptom-survey/index.md b/docs/symptom-survey/index.md index ec926dea3..1c2f46354 100644 --- a/docs/symptom-survey/index.md +++ b/docs/symptom-survey/index.md @@ -1,110 +1,113 @@ ---- -title: COVID-19 Trends and Impact Survey -has_children: true -nav_order: 6 ---- - -# COVID-19 Trends and Impact Survey - -Since April 2020, Delphi has conducted a voluntary survey about COVID-19, -distributed daily to users in the United States via a partnership with Facebook. -This survey asks respondents about COVID-like symptoms, their behavior (such as -social distancing), mental health, and economic and health impacts they have -experienced as a result of the pandemic. A high-level overview of the survey is -posted [on the COVIDcast website](https://delphi.cmu.edu/covid19/ctis/), and an -international version is [conducted by the University of -Maryland](https://covidmap.umd.edu/). Data collection [ceased on June 25, -2022](end-of-survey.md). - -The [CTIS Methodology -Report](https://dataforgood.facebook.com/dfg/resources/CTIS-methodology-report) -describes the survey design, data collection process, weighting, and aggregation -processes, and is the primary reference for researchers working with the survey -data. This website describes details specific to the US version of the survey -and documents the individual response data, which is available to researchers -with a signed Data Use Agreement. If you are a researcher and would like to get -access to the data, see our page on getting [data access](data-access.md). - -If you have questions about the survey or getting access to data, contact us at -. - -## Results - -The [survey results dashboard](https://delphi.cmu.edu/covidcast/survey-results/) -provides a high-level summary of survey results. Geographically aggregated data -from this survey is publicly available through the [COVIDcast API](../api/covidcast.md) -as the [`fb-survey` data source](../api/covidcast-signals/fb-survey.md). Demographic breakdowns of survey -data are publicly available as [downloadable contingency tables](contingency-tables.md). - -CTIS data has been used in [numerous peer-reviewed publications](publications.md). - -## Credits - -The US COVID-19 Trends and Impact Survey (CTIS) is a project of the [Delphi -Group](https://delphi.cmu.edu/) at Carnegie Mellon University. Team members -include: - -* [Alex Reinhart](https://www.refsmmat.com/), Principal Investigator -* Wichada La Motte-Kerr, Survey Coordinator (2020-2022) -* Robin Mejia, survey advisor -* Nat DeFries, statistical developer and data engineer -* Eu Jing Chua (2020-2021) and Mashrin Srivastava (2021-2022), data analysis - interns -* plus support from many members of the [Delphi - team](https://delphi.cmu.edu/about/team/) - -The survey protocol is reviewed by the Carnegie Mellon University Institutional -Review Board. - -The support of several institutions makes the survey possible. Facebook supports -the survey through recruitment (participants are invited via their News Feed), -survey sampling and weighting procedures, technical assistance in survey design -and implementation, and coordination with researchers and public health -officials. The University of Maryland's Social Data Science Center conducts a -[global version of the survey](https://covidmap.umd.edu/), and we coordinate -closely on survey design and implementation. Delphi collects, aggregates, and -distributes the US survey data, and retains ultimate responsibility for the US -survey instrument and data. - -We develop the survey collaboratively with data users, public health officials, -and others. If you are interested in getting involved, see our -[collaboration and survey revision information](collaboration-revision.md). - -## Citing the Survey - -Researchers who use the US survey data for research are asked to credit and cite -the survey in publications based on the data. Specifically, we ask that you: - -1. Include the acknowledgment "This research is based on survey results from - Carnegie Mellon University’s Delphi Group." -2. Cite our paper describing the survey: - - > Joshua A. Salomon, Alex Reinhart, Alyssa Bilinski, Eu Jing Chua, Wichada - > La Motte-Kerr, Minttu M. Rönn, Marissa Reitsma, Katherine Ann Morris, - > Sarah LaRocca, Tamar Farag, Frauke Kreuter, Roni Rosenfeld, and Ryan J. - > Tibshirani (2021). "The US COVID-19 Trends and Impact Survey: Continuous - > real-time measurement of COVID-19 symptoms, risks, protective behaviors, - > testing, and vaccination", *Proceedings of the National Academy of - > Sciences* 118 (51) e2111454118. - -3. The data use agreement requires that if you disclose survey microdata, Delphi - must agree on the aggregation method that you will use to ensure reported - estimates do not disclose any individual identifiable information, including - individual survey results. If you are unsure whether a particular aggregation - will prevent disclosure of individual survey results, please email us at - . -4. Finally, send a copy of your publication, once it appears publicly as a - preprint or journal article, to . - -When referring to the survey in text, we prefer the following formats: - -* Long form (such as in an introduction or methods description): "The Delphi - Group at Carnegie Mellon University U.S. COVID-19 Trends and Impact Survey, in - partnership with Facebook". -* Short form (used after the long form has been introduced): "The U.S. COVID-19 - Trends and Impact Survey" -* Acronym form: "Delphi US CTIS" - -Prior to July 2021, the survey was known as the COVID Symptom Survey (CSS), and -some older documentation and publications may still refer to this name. We -prefer that new publications and materials refer to the new name. +--- +title: inactive COVID-19 Trends and Impact Survey +nav_order: 4 +--- + +# COVID-19 Trends and Impact Survey (CTIS) + +Since April 2020, Delphi has conducted a voluntary survey about COVID-19, +distributed daily to users in the United States via a partnership with Facebook. +This survey asks respondents about COVID-like symptoms, their behavior (such as +social distancing), mental health, and economic and health impacts they have +experienced as a result of the pandemic. A high-level overview of the survey is +posted [on the Delphi website](https://delphi.cmu.edu/covid19/ctis/), +and an international version is +[conducted by the University of Maryland](https://covidmap.umd.edu/). +Data collection [ceased on June 25, 2022](end-of-survey.md). + +This survey was also known unofficially as the Facebook Survey. + +More survey details are also available [on the COVID-19 Trends and Impact Survey 2020-2022 (inactive) page](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/fb-survey.html) under the COVIDcast Main Endpoint's Data Source and Signals section of this API documentation site. + +The [CTIS Methodology +Report](https://dataforgood.facebook.com/dfg/resources/CTIS-methodology-report) +describes the survey design, data collection process, weighting, and aggregation +processes, and is the primary reference for researchers working with the survey +data. This website describes details specific to the US version of the survey +and documents the individual response data, which is available to researchers +with a signed Data Use Agreement. If you are a researcher and would like to get +access to the data, see our page on getting [data access](data-access.md). + +If you have questions about the survey or getting access to data, contact us at +. + +## Results + +The [survey results dashboard](https://delphi.cmu.edu/covidcast/survey-results/) +provides a high-level summary of survey results. Geographically aggregated data +from this survey is publicly available through the [COVIDcast API](../api/covidcast.md) +as the [`fb-survey` data source](../api/covidcast-signals/fb-survey.md). Demographic breakdowns of survey +data are publicly available as [downloadable contingency tables](contingency-tables.md). + +CTIS data has been used in [numerous peer-reviewed publications](publications.md). + +## Credits + +The US COVID-19 Trends and Impact Survey (CTIS) is a project of the [Delphi +Group](https://delphi.cmu.edu/) at Carnegie Mellon University. Team members +include: + +* [Alex Reinhart](https://www.refsmmat.com/), Principal Investigator +* Wichada La Motte-Kerr, Survey Coordinator (2020-2022) +* Robin Mejia, survey advisor +* Nat DeFries, statistical developer and data engineer +* Eu Jing Chua (2020-2021) and Mashrin Srivastava (2021-2022), data analysis + interns +* plus support from many members of the [Delphi + team](https://delphi.cmu.edu/about/team/) + +The survey protocol is reviewed by the Carnegie Mellon University Institutional +Review Board. + +The support of several institutions makes the survey possible. Facebook supports +the survey through recruitment (participants are invited via their News Feed), +survey sampling and weighting procedures, technical assistance in survey design +and implementation, and coordination with researchers and public health +officials. The University of Maryland's Social Data Science Center conducts a +[global version of the survey](https://covidmap.umd.edu/), and we coordinate +closely on survey design and implementation. Delphi collects, aggregates, and +distributes the US survey data, and retains ultimate responsibility for the US +survey instrument and data. + +We develop the survey collaboratively with data users, public health officials, +and others. If you are interested in getting involved, see our +[collaboration and survey revision information](collaboration-revision.md). + +## Citing the Survey + +Researchers who use the US survey data for research are asked to credit and cite +the survey in publications based on the data. Specifically, we ask that you: + +1. Include the acknowledgment "This research is based on survey results from + Carnegie Mellon University’s Delphi Group." +2. Cite our paper describing the survey: + + > Joshua A. Salomon, Alex Reinhart, Alyssa Bilinski, Eu Jing Chua, Wichada + > La Motte-Kerr, Minttu M. Rönn, Marissa Reitsma, Katherine Ann Morris, + > Sarah LaRocca, Tamar Farag, Frauke Kreuter, Roni Rosenfeld, and Ryan J. + > Tibshirani (2021). "The US COVID-19 Trends and Impact Survey: Continuous + > real-time measurement of COVID-19 symptoms, risks, protective behaviors, + > testing, and vaccination", *Proceedings of the National Academy of + > Sciences* 118 (51) e2111454118. + +3. The data use agreement requires that if you disclose survey microdata, Delphi + must agree on the aggregation method that you will use to ensure reported + estimates do not disclose any individual identifiable information, including + individual survey results. If you are unsure whether a particular aggregation + will prevent disclosure of individual survey results, please email us at + . +4. Finally, send a copy of your publication, once it appears publicly as a + preprint or journal article, to . + +When referring to the survey in text, we prefer the following formats: + +* Long form (such as in an introduction or methods description): "The Delphi + Group at Carnegie Mellon University U.S. COVID-19 Trends and Impact Survey, in + partnership with Facebook". +* Short form (used after the long form has been introduced): "The U.S. COVID-19 + Trends and Impact Survey" +* Acronym form: "Delphi US CTIS" + +Prior to July 2021, the survey was known as the COVID Symptom Survey (CSS), and +some older documentation and publications may still refer to this name. We +prefer that new publications and materials refer to the new name. diff --git a/docs/symptom-survey/limitations.md b/docs/symptom-survey/limitations.md index 42d995864..475956179 100644 --- a/docs/symptom-survey/limitations.md +++ b/docs/symptom-survey/limitations.md @@ -1,6 +1,6 @@ --- title: Survey Limitations -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 9 --- diff --git a/docs/symptom-survey/modules.md b/docs/symptom-survey/modules.md index a13c550ed..0b334f5c2 100644 --- a/docs/symptom-survey/modules.md +++ b/docs/symptom-survey/modules.md @@ -1,6 +1,6 @@ --- title: Survey Modules & Randomization -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 7 --- diff --git a/docs/symptom-survey/problems.md b/docs/symptom-survey/problems.md index 57e903a07..94576191d 100644 --- a/docs/symptom-survey/problems.md +++ b/docs/symptom-survey/problems.md @@ -1,6 +1,6 @@ --- title: Data and Sampling Errors -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 8 --- diff --git a/docs/symptom-survey/publications.md b/docs/symptom-survey/publications.md index 9144e88c5..d6ccf23be 100644 --- a/docs/symptom-survey/publications.md +++ b/docs/symptom-survey/publications.md @@ -1,6 +1,6 @@ --- title: Publications -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 10 --- diff --git a/docs/symptom-survey/server-access.md b/docs/symptom-survey/server-access.md index 62f91d0ea..c27b3e15b 100644 --- a/docs/symptom-survey/server-access.md +++ b/docs/symptom-survey/server-access.md @@ -1,6 +1,6 @@ --- title: SFTP Server Access -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 2 --- diff --git a/docs/symptom-survey/survey-files.md b/docs/symptom-survey/survey-files.md index d181449a1..e2bf0ed44 100644 --- a/docs/symptom-survey/survey-files.md +++ b/docs/symptom-survey/survey-files.md @@ -1,6 +1,6 @@ --- title: Response Files -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 3 --- diff --git a/docs/symptom-survey/weights.md b/docs/symptom-survey/weights.md index 1acc6785a..3cd1c60ee 100644 --- a/docs/symptom-survey/weights.md +++ b/docs/symptom-survey/weights.md @@ -1,6 +1,6 @@ --- title: Survey Weights -parent: COVID-19 Trends and Impact Survey +parent: inactive COVID-19 Trends and Impact Survey nav_order: 5 ---