From 335f037a2e61e3e9e52dc16680a13d674f7c6ebe Mon Sep 17 00:00:00 2001 From: minhkhul Date: Tue, 17 Jan 2023 14:24:02 -0500 Subject: [PATCH 1/4] mark inactive indicators on api documentation --- docs/api/covidcast-signals/covid-act-now.md | 2 +- docs/api/covidcast-signals/quidel.md | 2 +- docs/api/covidcast-signals/usa-facts.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/api/covidcast-signals/covid-act-now.md b/docs/api/covidcast-signals/covid-act-now.md index f56ecf015..72a5a9a20 100644 --- 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: Data Sources and Signals +parent: Inactive Signals grand_parent: COVIDcast Main Endpoint --- diff --git a/docs/api/covidcast-signals/quidel.md b/docs/api/covidcast-signals/quidel.md index 5f003904f..24642d15a 100644 --- a/docs/api/covidcast-signals/quidel.md +++ b/docs/api/covidcast-signals/quidel.md @@ -1,6 +1,6 @@ --- title: Quidel -parent: Data Sources and Signals +parent: Inactive Signals grand_parent: COVIDcast Main Endpoint --- diff --git a/docs/api/covidcast-signals/usa-facts.md b/docs/api/covidcast-signals/usa-facts.md index fc68c2dea..e0160cfde 100644 --- 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: Data Sources and Signals +parent: Inactive Signals grand_parent: COVIDcast Main Endpoint --- From f4bdbeb3d5f16036b1c51d6e8360db9fe3e4d505 Mon Sep 17 00:00:00 2001 From: minhkhul Date: Tue, 17 Jan 2023 16:40:57 -0500 Subject: [PATCH 2/4] changes to quidel --- docs/api/covidcast-signals/quidel-inactive.md | 52 +++++++++++ docs/api/covidcast-signals/quidel.md | 33 +------ docs/api/covidcast-signals/safegraph.md | 87 ------------------- 3 files changed, 54 insertions(+), 118 deletions(-) create mode 100644 docs/api/covidcast-signals/quidel-inactive.md delete mode 100644 docs/api/covidcast-signals/safegraph.md diff --git a/docs/api/covidcast-signals/quidel-inactive.md b/docs/api/covidcast-signals/quidel-inactive.md new file mode 100644 index 000000000..19b98ee6a --- /dev/null +++ b/docs/api/covidcast-signals/quidel-inactive.md @@ -0,0 +1,52 @@ +--- +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} + + +## 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 24642d15a..187bf81a1 100644 --- a/docs/api/covidcast-signals/quidel.md +++ b/docs/api/covidcast-signals/quidel.md @@ -157,34 +157,5 @@ 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 - -* **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 | +## Flu Tests (inactive) +These signals were updated until May 19, 2020. Documentation is still available on the [inactive Safegraph page](quidel-inactive.md). \ No newline at end of file diff --git a/docs/api/covidcast-signals/safegraph.md b/docs/api/covidcast-signals/safegraph.md deleted file mode 100644 index 3da66ed79..000000000 --- a/docs/api/covidcast-signals/safegraph.md +++ /dev/null @@ -1,87 +0,0 @@ ---- -title: SafeGraph -parent: Data Sources and Signals -grand_parent: COVIDcast Main Endpoint ---- - -# SafeGraph -{: .no_toc} -* **Source name:** `safegraph` -* **Available for:** county, MSA, HRR, state (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) - -This data source uses data reported by [SafeGraph](https://www.safegraph.com/) -using anonymized location data from mobile phones. SafeGraph provides several -different datasets to eligible researchers. We currently surface signals from one such -dataset. - -## Table of contents -{: .no_toc .text-delta} - -1. TOC -{:toc} - -## SafeGraph Social Distancing Metrics (Inactive) - -These signals were updated until April 19th, 2021, when Safegraph ceased updating the dataset. -Documentation for these signals is still available on the [inactive Safegraph page](safegraph-inactive.md). - -## SafeGraph Weekly Patterns - -* **Earliest issue available:** November 30, 2020 -* **Number of data revisions since June 23, 2020:** 0 -* **Date of last change:** never - -Data source based on [Weekly -Patterns](https://docs.safegraph.com/docs/weekly-patterns) dataset. SafeGraph -provides this data for different points of interest -([POIs](https://docs.safegraph.com/v4.0/docs#section-core-places)) considering -individual census block groups, using differential privacy to protect individual -people's data privacy. - -Delphi gathers the number of daily visits to POIs of certain types(bars, -restaurants, etc.) from SafeGraph's Weekly Patterns data at the 5-digit ZipCode -level, then aggregates and reports these features to the county, MSA, HRR, and -state levels. The aggregated data is freely available through the COVIDcast API. - -For precise definitions of the quantities below, consult the [SafeGraph Weekly -Patterns documentation](https://docs.safegraph.com/docs/weekly-patterns). - -| Signal | Description | -| --- | --- | -| `bars_visit_num` | The number of daily visits made by those with SafeGraph's apps to bar-related POIs in a certain region
**Earliest date available:** 01/01/2019 | -| `bars_visit_prop` | The number of daily visits made by those with SafeGraph's apps to bar-related POIs in a certain region, per 100,000 population
**Earliest date available:** 01/01/2019 | -| `restaurants_visit_num` | The number of daily visits made by those with SafeGraph's apps to restaurant-related POIs in a certain region
**Earliest date available:** 01/01/2019 | -| `restaurants_visit_prop` | The number of daily visits made by those with SafeGraph's apps to restaurant-related POIs in a certain region, per 100,000 population
**Earliest date available:** 01/01/2019 | - -SafeGraph delivers the number of daily visits to U.S. POIs, the details of which -are described in the [Places -Manual](https://readme.safegraph.com/docs/places-manual#section-placekey) -dataset. Delphi aggregates the number of visits to certain types of places, -such as bars (places with [NAICS code = -722410](https://www.census.gov/cgi-bin/sssd/naics/naicsrch?input=722410&search=2017+NAICS+Search&search=2017)) -and restaurants (places with [NAICS code = -722511](https://www.census.gov/cgi-bin/sssd/naics/naicsrch)). For example, -Adagio Teas is coded as a bar because it serves alcohol, while Napkin Burger is -considered to be a full-service restaurant. More information on NAICS codes is -available from the [US Census Bureau: North American Industry Classification -System](https://www.census.gov/eos/www/naics/index.html). - -The number of POIs coded as bars is much smaller than the number of POIs coded as restaurants. -SafeGraph's Weekly Patterns data consistently lacks data on bar visits for Alaska, Delaware, Maine, North Dakota, New Hampshire, South Dakota, Vermont, West Virginia, and Wyoming. -For certain dates, bar visits data is also missing for District of Columbia, Idaho and Washington. Restaurant visits data is available for all of the states, as well as the District of Columbia and Puerto Rico. - -### Lag - -SafeGraph provides newly updated data for the previous week every Wednesday, -meaning estimates for a specific day are only available 3-9 days later. It may -take up to an additional day for SafeGraph's data to be ingested into the -COVIDcast API. - -## Limitations - -SafeGraph's Social Distancing Metrics and Weekly Patterns are based on mobile devices that are members of SafeGraph panels, which is not necessarily the same thing as measuring the general public. These counts do not represent absolute counts, and only count visits by members of the panel in that region. This can result in several biases: - -* **Geographic bias.** If some regions have a greater density of SafeGraph panel members as a percentage of the population than other regions, comparisons of metrics between regions may be biased. Regions with more SafeGraph panel members will appear to have more visits counted, even if the rate of visits in the general population is the same. -* **Demographic bias.** SafeGraph panels may not be representative of the local population as a whole. For example, [some research suggests](https://doi.org/10.1145/3442188.3445881) that "older and non-white voters are less likely to be captured by mobility data", so this data will not accurately reflect behavior in those populations. Since population demographics vary across the United States, this can also contribute to geographic biases. From 6cbb9e1603ac553ffaace33b4fc6eef3f1f94d9f Mon Sep 17 00:00:00 2001 From: minhkhul Date: Tue, 17 Jan 2023 16:43:27 -0500 Subject: [PATCH 3/4] tested change to quidel --- docs/api/covidcast-signals/quidel.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/covidcast-signals/quidel.md b/docs/api/covidcast-signals/quidel.md index 187bf81a1..259eba28b 100644 --- a/docs/api/covidcast-signals/quidel.md +++ b/docs/api/covidcast-signals/quidel.md @@ -1,6 +1,6 @@ --- title: Quidel -parent: Inactive Signals +parent: Data Sources and Signals grand_parent: COVIDcast Main Endpoint --- From 9f4b5fa0b31029fcadd002a257e71f0aea5737a7 Mon Sep 17 00:00:00 2001 From: Katie Mazaitis Date: Tue, 17 Jan 2023 17:13:03 -0500 Subject: [PATCH 4/4] s/Safegraph/Quidel on quidel.md --- docs/api/covidcast-signals/quidel.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/covidcast-signals/quidel.md b/docs/api/covidcast-signals/quidel.md index 259eba28b..54296dbb3 100644 --- a/docs/api/covidcast-signals/quidel.md +++ b/docs/api/covidcast-signals/quidel.md @@ -158,4 +158,4 @@ no data is reported for that area on that day; an API query for all reported geo that day will not include it. ## Flu Tests (inactive) -These signals were updated until May 19, 2020. Documentation is still available on the [inactive Safegraph page](quidel-inactive.md). \ No newline at end of file +These signals were updated until May 19, 2020. Documentation is still available on the [inactive Quidel page](quidel-inactive.md). \ No newline at end of file