Merge pull request #1606 from cmu-delphi/release/delphi-epidata-4.1.31

melange396 · web-flow · commit 838835809a8c · 2025-02-25T18:04:22.000-05:00
Release Delphi Epidata 4.1.31
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.30
+current_version = 4.1.31
 commit = False
 tag = False
 
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -103,7 +103,7 @@ jobs:
         with:
           node-version: '16.x'
       - name: Cache Node.js modules
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ~/.npm # npm cache files are stored in `~/.npm` on Linux/macOS
           key: ${{ runner.OS }}-node2-${{ hashFiles('**/package-lock.json') }}
diff --git a/.github/workflows/release-helper.yml b/.github/workflows/release-helper.yml
@@ -121,7 +121,7 @@ jobs:
         with:
           node-version: "16.x"
       - name: Cache Node.js modules
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ~/.npm # npm cache files are stored in `~/.npm` on Linux/macOS
           key: ${{ runner.OS }}-node2-${{ hashFiles('**/package-lock.json') }}
diff --git a/.github/workflows/update_gdocs_data.yml b/.github/workflows/update_gdocs_data.yml
@@ -14,7 +14,7 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pipd-${{ hashFiles('requirements.dev.txt') }}
diff --git a/dev/local/setup.cfg b/dev/local/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.30
+version = 4.1.31
 
 [options]
 packages =
diff --git a/docs/api/01meta.md b/docs/api/01meta.md
@@ -1,11 +1,12 @@
 ---
-title: <i>inactive</i> Metadata
+title: <i>inactive</i> Epidata Metadata
 parent: Data Sources and Signals
 grand_parent: Other Endpoints (COVID-19 and Other Diseases)
 nav_order: 2
+permalink: api/meta.html
 ---
 
-# API Metadata
+# Epidata Metadata
 
 This is the documentation of the API for accessing the API Metadata (`meta`) for `fluview`, `twitter`, `wiki`,
 and `delphi` endpoints of the [Delphi](https://delphi.cmu.edu/)'s epidemiological data.
diff --git a/docs/api/covidcast-signals/covid-trends-and-impact-survey.md b/docs/api/covidcast-signals/covid-trends-and-impact-survey.md
@@ -3,9 +3,10 @@ title: <i>inactive</i> COVID-19 Trends and Impact Survey
 parent: Data Sources and Signals
 grand_parent: Main Endpoint (COVIDcast)
 nav_order: 2
+permalink: api/covidcast-signals/fb-survey.html
 ---
 
-# COVID-19 Trends and Impact Survey 2020-2022 (Facebook Survey)
+# COVID-19 Trends and Impact Survey (CTIS)
 {: .no_toc}
 
 * **Source name:** `fb-survey`
@@ -28,6 +29,8 @@ shared back to Facebook. See our [surveys
 page](https://delphi.cmu.edu/covid19/ctis/) for more detail about how the
 surveys work and how they are used outside the COVIDcast API.
 
+This survey was also known unofficially as the Facebook Survey.
+
 As of November 2021, the average number of Facebook survey responses we
 received each day was about 40,000. The survey ran from April 6, 2020 to June
 25, 2022, collecting roughly 29.5 million responses in the United States in that
diff --git a/docs/api/covidcast-signals/dsew-cpr.md b/docs/api/covidcast-signals/dsew-cpr.md
@@ -83,5 +83,5 @@ The CPR is prepared with an internal lag of 1-2 days for most signals. The file
 
 ## Source and Licensing
 
-This indicator mirrors and lightly aggregates data originally published by the Data Strategy and Execution Workgroup via [HealthData.gov](https://healthdata.gov/). As a work of the US government, the original data is in the [public domain](https://www.usa.gov/government-works).
+These indicators mirror and lightly aggregate data originally published by the Data Strategy and Execution Workgroup via [HealthData.gov](https://healthdata.gov/). As a work of the US government, the original data is in the [public domain](https://www.usa.gov/government-works).
 
diff --git a/docs/api/covidcast-signals/hhs.md b/docs/api/covidcast-signals/hhs.md
@@ -1,11 +1,11 @@
 ---
-title: <i>inactive</i> Department of Health & Human Services
+title: <i>inactive</i> HHS Hospitalizations from NHSN
 parent: Data Sources and Signals
 grand_parent: Main Endpoint (COVIDcast)
 nav_order: 2
 ---
 
-# Department of Health & Human Services
+# Department of Health & Human Services Hospitalizations
 {: .no_toc}
 
 * **Source name:** `hhs`
@@ -17,18 +17,19 @@ nav_order: 2
 * **License:** [Public Domain US Government](https://www.usa.gov/government-works)
 
 The U.S. Department of Health & Human Services (HHS) publishes several
-datasets on patient impact and hospital capacity. One of these
+datasets on patient impact and hospital capacity. The data is made available
+to HHS through the CDC’s National Healthcare Safety Network (NHSN). One of these
 datasets is mirrored in Epidata at the following endpoint:
 
 * [COVID-19 Hospitalization: States](../covid_hosp.md) - daily resolution, state aggregates
 
 That dataset contains dozens of columns that break down hospital
 resource usage in different ways.
 
-This indicator makes available several commonly-used columns and combinations of
+These indicators make available several commonly-used columns and combinations of
 columns, aggregated geographically. In particular, we include the sum of all
 adult and pediatric COVID-19 hospital admissions. This sum is used as the
-"ground truth" for hospitalizations by the 
+"ground truth" for hospitalizations by the
 [COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub/blob/master/data-processed/README.md#hospitalizations).
 We also include influenza hospital admissions.
 
@@ -115,7 +116,7 @@ is first published.
 
 ## Source and Licensing
 
-This indicator mirrors and lightly aggregates data originally
-published by the U.S. Department of Health & Human Services. 
-As a work of the US government, the original data is in the 
+These indicators mirror and lightly aggregate data originally
+published by the U.S. Department of Health & Human Services.
+As a work of the US government, the original data is in the
 [public domain](https://www.usa.gov/government-works).
diff --git a/docs/api/covidcast-signals/nhsn.md b/docs/api/covidcast-signals/nhsn.md
@@ -31,12 +31,21 @@ For reference dates in May 2024, NHSN received data from 78% of US EDs.
 State and nation-level values are pulled directly from the source; HHS-level values are aggregated up from the state level.
 
 
-| Signal                          | Description                                                                                                                                                                         |
-|---------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `confirmed_admissions_covid_ew`              | Total number of patients hospitalized with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week. **Earliest date available:** 2020-08-08                                                                                                     |
-| `confirmed_admissions_covid_ew_prelim`          | Total number of patients hospitalized with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week. <br/> **Earliest date available:** 2020-08-08  |
-| `confirmed_admissions_flu_ew`           | Total number of patients hospitalized with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week.  <br/> **Earliest date available:** 2020-08-08                                                                                       |
-| `confirmed_admissions_flu_ew_prelim`     | Total number of patients hospitalized with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week. <br/> **Earliest date available:** 2020-08-08 |
+| Signal                                         | Description                                                                                                                                                                                                                                                                          |
+|------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `confirmed_admissions_covid_ew`                | Total number of patients hospitalized with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week. <br/> **Earliest date available:** 2020-08-08                    |
+| `hosprep_confirmed_admissions_covid_ew`        | Total number of number of hospitals reporting new admissions with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week.<br/> **Earliest date available:** 2020-08-08                                                                                                           |
+| `confirmed_admissions_covid_ew_prelim`         | Total number of patients hospitalized with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week. <br/> **Earliest date available:** 2020-08-08                                   |
+| `hosprep_confirmed_admissions_covid_ew_prelim` | Total number of number of hospitals reporting new admissions with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week. <br/> **Earliest date available:** 2020-08-08            |
+| `confirmed_admissions_flu_ew`                  | Total number of patients hospitalized with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week.  <br/> **Earliest date available:** 2020-08-08                  |
+| `hosprep_confirmed_admissions_flu_ew`          | Total number of hospitals reporting new admissions with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week.  <br/> **Earliest date available:** 2020-08-08     |
+| `confirmed_admissions_flu_ew_prelim`           | Total number of patients hospitalized with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week. <br/> **Earliest date available:** 2020-08-08                            |
+| `hosprep_confirmed_admissions_flu_ew_prelim`   | Total number of number of hospitals reporting new admissions with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week. <br/> **Earliest date available:** 2020-08-08     |
+| `confirmed_admissions_rsv_ew`                  | Total number of patients hospitalized with confirmed RSV over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week.  <br/> **Earliest date available:** 2020-08-08                        |
+| `hosprep_confirmed_admissions_rsv_ew`          | Total number of number of hospitals reporting new admissions with confirmed RSV over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week.  <br/> **Earliest date available:** 2020-08-08 |
+| `confirmed_admissions_rsv_ew_prelim`           | Total number of patients hospitalized with confirmed RSV over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week. <br/> **Earliest date available:** 2020-08-08                                  |
+| `hosprep_confirmed_admissions_rsv_ew_prelim`   | Total number of number of hospitals reporting new admissions with confirmed RSV over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week.  <br/> **Earliest date available:** 2020-08-08          |
+
 
 ## Table of Contents
 {: .no_toc .text-delta}
@@ -88,6 +97,10 @@ Only hospitals indicated as active reporters in NHSN are included.
 Between reference dates 2024-05-01 and 2024-10-31, reported hospitalizations may not be fully representative, since reporting was voluntary.
 See the [missingness section](#missingness) for more information about voluntary and mandatory reporting periods.
 
+Data for RSV from the pre-October 31, 2024 voluntary reporting period is particularly low quality. Only a tiny fraction of hospitals reported RSV-associated admissions such that they are undercounted by a factor of perhaps 100. For historical RSV-associated admissions, see the [CDC's RSV-NET](https://www.cdc.gov/rsv/php/surveillance/rsv-net.html) (not currently mirrored by Delphi).
+
+For earlier issue dates certain signals may not be available. The earliest issue date with all the current signals available is epiweek 202451
+
 Standard errors and sample sizes are not applicable to these metrics.
 
 
diff --git a/docs/api/covidcast-signals/youtube-survey.md b/docs/api/covidcast-signals/youtube-survey.md
@@ -42,7 +42,7 @@ note that values from the same dates differ between the two surveys for
 
 As of late April 2020, the number of Youtube survey responses we received each
 day was 4-7 thousand. This was not enough coverage to report at finer
-geographic levels, so this indicator only reports at the state level. The
+geographic levels, so these indicators only report at the state level. The
 survey ran from April 21, 2020 to June 17, 2020, collecting about 159
 thousand responses in the United States in that time.
 
@@ -122,7 +122,7 @@ available for more locations than the raw signals.
 
 ## Lag and Backfill
 
-This indicator has a lag of 2 days. Reported values can be revised for one
+These indicators have a lag of 2 days. Reported values can be revised for one
 day (corresponding to a lag of 3 days), due to how we receive survey
 responses. However, these tend to be associated with minimal changes in
 value.
@@ -172,5 +172,5 @@ longer time period.
 
 ## Source and Licensing
 
-This indicator aggregates responses from a Delphi-run survey that is hosted on the Youtube platform.
+These indicators aggregate responses from a Delphi-run survey that is hosted on the Youtube platform.
 The data is licensed as [CC BY-NC](../covidcast_licensing.md#creative-commons-attribution-noncommercial).
diff --git a/docs/api/dengue_digital_surveillance.md b/docs/api/dengue_digital_surveillance.md
@@ -3,6 +3,7 @@ title: <i>inactive</i> Dengue Digital Surveillance
 parent: Data Sources and Signals
 grand_parent: Other Endpoints (COVID-19 and Other Diseases)
 nav_order: 2
+permalink: api/dengue_sensors.html
 ---
 
 # Dengue Digital Surveillance Sensors
diff --git a/docs/api/digital_surveillance_sensors.md b/docs/api/digital_surveillance_sensors.md
@@ -3,6 +3,7 @@ title: <i>inactive</i> Digital Surveillance Sensors
 parent: Data Sources and Signals
 grand_parent: Other Endpoints (COVID-19 and Other Diseases)
 nav_order: 2
+permalink: api/sensors.html
 ---
 
 # Digital Surveillance Sensors
diff --git a/docs/api/fluview_meta.md b/docs/api/fluview_meta.md
@@ -1,11 +1,11 @@
 ---
-title: FluView metadata
+title: FluView Metadata
 parent: Data Sources and Signals
 grand_parent: Other Endpoints (COVID-19 and Other Diseases)
 nav_order: 1
 ---
 
-# FluView metadata
+# FluView Metadata
 
 This is the API documentation for accessing the FluView metadata
 (`fluview_meta`) endpoint of [Delphi](https://delphi.cmu.edu/)'s epidemiological
diff --git a/docs/api/ili_nearby_nowcast.md b/docs/api/ili_nearby_nowcast.md
@@ -3,6 +3,7 @@ title: <i>inactive</i> ILI Nearby Nowcast
 parent: Data Sources and Signals
 grand_parent: Other Endpoints (COVID-19 and Other Diseases)
 nav_order: 2
+permalink: api/nowcast.html
 ---
 
 # ILI Nearby Nowcast
diff --git a/docs/api/norostat_meta.md b/docs/api/norostat_meta.md
@@ -3,6 +3,7 @@ title: <i>inactive</i> NoroSTAT Metadata
 parent: Data Sources and Signals
 grand_parent: Other Endpoints (COVID-19 and Other Diseases)
 nav_order: 2
+permalink: api/meta_norostat.html
 ---
 
 # NoroSTAT Metadata
diff --git a/src/client/delphi_epidata.R b/src/client/delphi_epidata.R
@@ -15,7 +15,7 @@ Epidata <- (function() {
   # API base url
   BASE_URL <- getOption('epidata.url', default = 'https://api.delphi.cmu.edu/epidata/')
 
-  client_version <- '4.1.30'
+  client_version <- '4.1.31'
 
   auth <- getOption("epidata.auth", default = NA)
 
diff --git a/src/client/delphi_epidata.js b/src/client/delphi_epidata.js
@@ -22,7 +22,7 @@
   }
 })(this, function (exports, fetchImpl, jQuery) {
   const BASE_URL = "https://api.delphi.cmu.edu/epidata/";
-  const client_version = "4.1.30";
+  const client_version = "4.1.31";
 
   // Helper function to cast values and/or ranges to strings
   function _listitem(value) {
diff --git a/src/client/packaging/npm/package.json b/src/client/packaging/npm/package.json
@@ -2,7 +2,7 @@
   "name": "delphi_epidata",
   "description": "Delphi Epidata API Client",
   "authors": "Delphi Group",
-  "version": "4.1.30",
+  "version": "4.1.31",
   "license": "MIT",
   "homepage": "https://github.com/cmu-delphi/delphi-epidata",
   "bugs": {
diff --git a/src/server/_config.py b/src/server/_config.py
@@ -7,7 +7,7 @@
 
 load_dotenv()
 
-VERSION = "4.1.30"
+VERSION = "4.1.31"
 
 MAX_RESULTS = int(10e6)
 MAX_COMPATIBILITY_RESULTS = int(3650)
diff --git a/src/server/endpoints/covidcast_utils/db_signals.csv b/src/server/endpoints/covidcast_utils/db_signals.csv
diff --git a/tasks.py b/tasks.py

Original file line number	Diff line number	Diff line change
`@@ -83,5 +83,5 @@ The CPR is prepared with an internal lag of 1-2 days for most signals. The file`
`83`	`83`
`84`	`84`	`## Source and Licensing`
`85`	`85`
`86`		`-This indicator mirrors and lightly aggregates data originally published by the Data Strategy and Execution Workgroup via [HealthData.gov](https://healthdata.gov/). As a work of the US government, the original data is in the [public domain](https://www.usa.gov/government-works).`
	`86`	`+These indicators mirror and lightly aggregate data originally published by the Data Strategy and Execution Workgroup via [HealthData.gov](https://healthdata.gov/). As a work of the US government, the original data is in the [public domain](https://www.usa.gov/government-works).`
`87`	`87`
Original file line number	Diff line number	Diff line change
`@@ -22,7 +22,7 @@`
`22`	`22`	`}`
`23`	`23`	`})(this, function (exports, fetchImpl, jQuery) {`
`24`	`24`	`const BASE_URL = "https://api.delphi.cmu.edu/epidata/";`
`25`		`- const client_version = "4.1.30";`
	`25`	`+ const client_version = "4.1.31";`
`26`	`26`
`27`	`27`	`// Helper function to cast values and/or ranges to strings`
`28`	`28`	`function _listitem(value) {`