Merge pull request #1410 from cmu-delphi/release/delphi-epidata-4.1.20

Release Delphi Epidata 4.1.20

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.19
+current_version = 4.1.20
 commit = False
 tag = False
 

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.19
+version = 4.1.20
 
 [options]
 packages =

docs/_config.yml

@@ -45,7 +45,7 @@ footer_content: "Copyright &copy; 2020, <a href='https://delphi.cmu.edu'>Delphi
 
 heading_anchors: true
 
-
+favicon_ico: "favicon.ico"
 # Exclude from processing.
 # The following items will not be processed, by default. Create a custom list
 # to override the default setting.

docs/api/covidcast-signals/chng.md

@@ -183,6 +183,8 @@ a median delta of 1% or less), as most major revisions have already occurred.
 
 We are currently working on adjustments to correct for this.
 
+See our [blog post](https://delphi.cmu.edu/blog/2020/11/05/a-syndromic-covid-19-indicator-based-on-insurance-claims-of-outpatient-visits/#backfill) for more information on backfill.
+
 ## Limitations
 
 This data source is based on data provided to us by Change Healthcare. Change

docs/api/covidcast-signals/dsew-cpr.md

@@ -1,6 +1,6 @@
 ---
 title: Data Strategy and Execution Workgroup Community Profile Report
-parent: Data Sources and Signals
+parent: Inactive Signals
 grand_parent: COVIDcast Main Endpoint
 ---
 
@@ -27,9 +27,10 @@ County, MSA, state, and HHS-level values are pulled directly from CPR when avail
 | --- | --- |
 | `confirmed_admissions_covid_1d_7dav` | Number of adult and pediatric confirmed COVID-19 hospital admissions occurring each day. Smoothed using a 7-day average.  <br/> **Earliest date available:** 2019-12-16 for state, HHS, and nation; 2021-01-06 for MSA and county |
 | `confirmed_admissions_covid_1d_prop_7dav` | Number of adult and pediatric confirmed COVID-19 hospital admissions occurring each day, per 100,000 population. Smoothed using a 7-day average. <br/> **Earliest date available:** 2019-12-16 for state, HHS, and nation; 2021-01-06 for MSA and county |
+| `covid_naat_pct_positive_7dav` | "NAAT positivity rate is the number of positive [SARS-CoV-2 Nucleic Acid Amplification Test (NAAT)] tests divided by the number of [NAAT] tests performed and resulted. See the CDC's [coronavirus resources page](https://web.archive.org/web/20210602062946/https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/calculating-percent-positivity.html) for more information on this method. In rare cases, negative test numbers may be reported on a given day to correct previous numbers, and this sometimes results in a calculated test positivity of greater than 100%. In these cases, test positivity is capped at 100%.” - from the CPR data dictionary. <br/> **Earliest date available:** 2020-12-07
 | `people_full_vaccinated` | "People fully vaccinated includes those who have received two doses of the Pfizer-BioNTech or Moderna vaccine and those who have received one dose of the J&J/Janssen vaccine" - from the CPR data dictionary.  <br/> **Earliest date available:** 2021-01-15 at any geo level except MSA and 2021-04-01 at the MSA level.|
 | `people_booster_doses` |"The count of people who received a booster dose includes anyone who is fully vaccinated and has received another dose of COVID-19 vaccine since 2021-08-13. This includes people who received booster doses and people who received additional doses." - from the CPR data dictionary. <br/> **Earliest date available:** 2021-11-01 for state, HHS, and nation. Not available below state level. |
-| `doses_admin_7dav` | "Doses administered shown by date of report, not date of administration. ... [S]ubmitting entities will have the ability to update or delete previously submitted records using new functionality available in CDC’s Data Clearinghouse. Use of this new functionality may result in fluctuations across metrics as historical data are updated or deleted" - from the CPR data dictionary.  Smoothed using a 7-day average. <br/> **Earliest date available:** 2021-04-29 for state, HHS, and nation. Not available below state level. |
+| `doses_admin_7dav` | "Doses administered shown by date of report, not date of administration. ... [S]ubmitting entities will have the ability to update or delete previously submitted records using new functionality available in CDC’s Data Clearinghouse. Use of this new functionality may result in fluctuations across metrics as historical data are updated or deleted" - from the CPR data dictionary.  Smoothed using a 7-day average. <br/> **Earliest date available:** 2021-05-02 for state, HHS, and nation. Not available below state level. |
 | `booster_doses_admin_7dav` | "Doses administered shown by date of report, not date of administration. ... [S]ubmitting entities will have the ability to update or delete previously submitted records using new functionality available in CDC’s Data Clearinghouse. Use of this new functionality may result in fluctuations across metrics as historical data are updated or deleted" - from the CPR data dictionary. "[A] booster dose includes anyone who is fully vaccinated and has received another dose of COVID-19 vaccine since August 13, 2021. This includes people who received booster doses and people who received additional doses." - from the CPR data dictionary. Smoothed using a 7-day average.<br/> **Earliest date available:** 2021-11-01 for state, HHS, and nation. Not available below state level. |
 
 ## Table of contents

docs/api/covidcast-signals/google-symptoms.md

@@ -38,19 +38,19 @@ Until January 20, 2022, we had separate signals for symptoms Anosmia, Ageusia, a
 
 | Signal | Description |
 | --- | --- |
-| `s01_raw_search` | The average of Google search volume for related searches of symptom set _s01_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-01-01 |
-| `s01_smoothed_search` | The average of Google search volume for related searches of symptom set _s01_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-01-07 |
-| `s02_raw_search` | The average of Google search volume for related searches of symptom set _s02_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-01-01 |
-| `s02_smoothed_search` | The average of Google search volume for related searches of symptom set _s02_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-01-07 |
-| `s03_raw_search` | The average of Google search volume for related searches of symptom set _s03_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-01-01 |
-| `s03_smoothed_search` | The average of Google search volume for related searches of symptom set _s03_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-01-07 |
-| `s04_raw_search` | The average of Google search volume for related searches of symptom set _s04_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-01-01 |
-| `s04_smoothed_search` | The average of Google search volume for related searches of symptom set _s04_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-01-07 |
-| `s05_raw_search` | The average of Google search volume for related searches of symptom set _s05_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-01-01 |
-| `s05_smoothed_search` | The average of Google search volume for related searches of symptom set _s05_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-01-07 |
-| `s06_raw_search` | The average of Google search volume for related searches of symptom set _s06_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-01-01 |
-| `s06_smoothed_search` | The average of Google search volume for related searches of symptom set _s06_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-01-07 |
-| `scontrol_raw_search` | The average of Google search volume for related searches of symptom set _scontrol_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-01-01 |
+| `s01_raw_search` | The average of Google search volume for related searches of symptom set _s01_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-02-14 |
+| `s01_smoothed_search` | The average of Google search volume for related searches of symptom set _s01_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-02-20 |
+| `s02_raw_search` | The average of Google search volume for related searches of symptom set _s02_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-02-14 |
+| `s02_smoothed_search` | The average of Google search volume for related searches of symptom set _s02_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-02-20 |
+| `s03_raw_search` | The average of Google search volume for related searches of symptom set _s03_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-02-14 |
+| `s03_smoothed_search` | The average of Google search volume for related searches of symptom set _s03_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-02-20 |
+| `s04_raw_search` | The average of Google search volume for related searches of symptom set _s04_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-02-14 |
+| `s04_smoothed_search` | The average of Google search volume for related searches of symptom set _s04_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-02-20 |
+| `s05_raw_search` | The average of Google search volume for related searches of symptom set _s05_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-02-14 |
+| `s05_smoothed_search` | The average of Google search volume for related searches of symptom set _s05_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-02-20 |
+| `s06_raw_search` | The average of Google search volume for related searches of symptom set _s06_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-02-14 |
+| `s06_smoothed_search` | The average of Google search volume for related searches of symptom set _s06_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-02-20 |
+| `scontrol_raw_search` | The average of Google search volume for related searches of symptom set _scontrol_, in an arbitrary units that are normalized for overall search users. <br/> **Earliest date available:** 2020-02-14 |
 | `scontrol_smoothed_search` | The average of Google search volume for related searches of symptom set _scontrol_, in an arbitrary units that are normalized for overall search users, smoothed by 7-day average. <br/> **Earliest date available:** 2020-02-20 |
 | `anosmia_raw_search` |  Google search volume for anosmia-related searches, in arbitrary units that are normalized for overall search users. _This signal is no longer updated as of 20 January, 2022._ <br/> **Earliest date available:** 2020-02-13 |
 | `anosmia_smoothed_search` | Google search volume for anosmia-related searches, in arbitrary units that are normalized for overall search users, smoothed by 7-day average. _This signal is no longer updated as of 20 January, 2022._ <br/> **Earliest date available:** 2020-02-20 |

docs/api/covidcast-signals/hospital-admissions.md

@@ -60,6 +60,8 @@ in later data revisions (having a median delta of 10% or more). Estimates for
 dates more than 57 days in the past are expected to remain fairly static (having
 a median delta of 1% or less), as most major revisions have already occurred.
 
+See our [blog post](https://delphi.cmu.edu/blog/2020/11/05/a-syndromic-covid-19-indicator-based-on-insurance-claims-of-outpatient-visits/#backfill) for more information on backfill.
+
 ## Limitations
 
 This data source is based on electronic medical records and claims data provided

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 <- '4.1.19'
+  client_version <- '4.1.20'
 
   auth <- getOption("epidata.auth", default = NA)
 

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 = "4.1.19";
+  const client_version = "4.1.20";
 
   // Helper function to cast values and/or ranges to strings
   function _listitem(value) {

src/client/packaging/npm/package.json

@@ -2,7 +2,7 @@
   "name": "delphi_epidata",
   "description": "Delphi Epidata API Client",
   "authors": "Delphi Group",
-  "version": "4.1.19",
+  "version": "4.1.20",
   "license": "MIT",
   "homepage": "https://github.com/cmu-delphi/delphi-epidata",
   "bugs": {

src/client/packaging/pypi/delphi_epidata/__init__.py

@@ -1,4 +1,4 @@
 from .delphi_epidata import Epidata
 
 name = "delphi_epidata"
-__version__ = "4.1.19"
+__version__ = "4.1.20"

src/client/packaging/pypi/setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="delphi_epidata",
-    version="4.1.19",
+    version="4.1.20",
     author="David Farrow",
     author_email="[email protected]",
     description="A programmatic interface to Delphi's Epidata API.",

src/server/_config.py

@@ -7,7 +7,7 @@
 
 load_dotenv()
 
-VERSION = "4.1.19"
+VERSION = "4.1.20"
 
 MAX_RESULTS = int(10e6)
 MAX_COMPATIBILITY_RESULTS = int(3650)