Merge remote-tracking branch 'upstream/main' into main

Author: chinandrew

deploy.json

@@ -230,6 +230,15 @@
       "add-header-comment": true
     },
 
+    "// acquisition - covidcast_nowcast",
+    {
+      "type": "move",
+      "src": "src/acquisition/covidcast_nowcast/",
+      "dst": "[[package]]/acquisition/covidcast_nowcast/",
+      "match": "^.*\\.(py)$",
+      "add-header-comment": true
+    },
+
     "// run unit and coverage tests",
     {"type": "py3test"}
 

docs/Gemfile.lock

@@ -201,21 +201,23 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
-    mini_portile2 (2.4.0)
+    mini_portile2 (2.5.0)
     minima (2.5.1)
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
     minitest (5.14.1)
     multipart-post (2.1.1)
-    nokogiri (1.10.10)
-      mini_portile2 (~> 2.4.0)
+    nokogiri (1.11.1)
+      mini_portile2 (~> 2.5.0)
+      racc (~> 1.4)
     octokit (4.18.0)
       faraday (>= 0.9)
       sawyer (~> 0.8.0, >= 0.5.3)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     public_suffix (3.1.1)
+    racc (1.5.2)
     rb-fsevent (0.10.4)
     rb-inotify (0.10.1)
       ffi (~> 1.0)

docs/api/README.md

@@ -64,6 +64,8 @@ wholly or partially serve data under this license include:
 
 [![Creative Commons License](https://i.creativecommons.org/l/by/4.0/88x31.png)](https://creativecommons.org/licenses/by/4.0/)
 
+Please note that our `endpoint` parameters were previously referenced as `source` in our API. New users will now use the `endpoint` parameter when accessing our data. If you are a returning or continuous user you do not have to make any changes, as the parameter `source` still works as usual.
+
 ---
 
 # The API
@@ -152,7 +154,7 @@ The parameters available for each source are documented in each linked source-sp
 # Example URLs
 
 ### FluView on 2015w01 (national)
-https://delphi.cmu.edu/epidata/api.php?source=fluview&regions=nat&epiweeks=201501
+https://delphi.cmu.edu/epidata/api.php?endpoint=fluview&regions=nat&epiweeks=201501
 
 ```json
 {
@@ -182,7 +184,7 @@ https://delphi.cmu.edu/epidata/api.php?source=fluview&regions=nat&epiweeks=20150
 ```
 
 ### Wikipedia Access article "influenza" on 2020w01
-https://delphi.cmu.edu/epidata/api.php?source=wiki&language=en&articles=influenza&epiweeks=202001
+https://delphi.cmu.edu/epidata/api.php?endpoint=wiki&language=en&articles=influenza&epiweeks=202001
 
 ```json
 {

docs/api/covid_hosp.md

@@ -67,7 +67,7 @@ If `issues` is not specified, then the most recent issue is used by default.
 # Example URLs
 
 ### MA on 2020-05-10 (per most recent issue)
-https://delphi.cmu.edu/epidata/api.php?source=covid_hosp&states=MA&dates=20200510
+https://delphi.cmu.edu/epidata/api.php?endpoint=covid_hosp&states=MA&dates=20200510
 
 ```json
 {

docs/api/covid_hosp_facility_lookup.md

@@ -1,5 +1,5 @@
 ---
-title: COVID-19 Reported Patient Impact and Hospital Capacity: Facility lookup
+title: COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup
 parent: Epidata API (Other Diseases)
 ---
 
@@ -31,7 +31,7 @@ This data source provides metadata about healthcare facilities in the US.
 
 # The API
 
-The base URL is: https://delphi.cmu.edu/epidata/api.php
+The base URL is: https://delphi.cmu.edu/epidata/api.php?source=covid_hosp_facility_lookup
 
 See [this documentation](README.md) for details on specifying locations and dates.
 

docs/api/covidcast-signals/fb-survey.md

@@ -10,7 +10,7 @@ grand_parent: COVIDcast Epidata API
 * **Source name:** `fb-survey`
 * **Number of data revisions since 19 May 2020:** 1
 * **Date of last change:** [3 June 2020](../covidcast_changelog.md#fb-survey)
-* **Available for:** county, hrr, msa, state (see [geography coding docs](../covidcast_geography.md))
+* **Available for:** county, hrr, msa, state, 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)
 
@@ -324,16 +324,19 @@ also available. These have names beginning `smoothed_w`, such as
 | Signal | Description | Survey Item |
 | --- | --- | --- |
 | `smoothed_accept_covid_vaccine` | Estimated percentage of respondents who would definitely or probably choose to get vaccinated, if a COVID-19 vaccine were offered to them today. **Note:** Until January 6, 2021, all respondents answered this question; beginning on that date, only respondents who said they have not received a COVID vaccine are asked this question. | V3 |
+| `smoothed_covid_vaccinated` | Estimated percentage of respondents who have already received a vaccine for COVID-19. **Note:** The Centers for Disease Control compiles data on vaccine administration across the United States. This signal may differ from CDC data because of survey biases and should not be treated as authoritative. However, the survey signal is not subject to the lags and reporting problems in official vaccination data. | V1 |
 
-This indicator is based on questions added in Wave 6 of the survey, introduced
-on December 19, 2020. **Note:** As of January 2021, vaccination items on the
-survey are being revised in preparation for Wave 7. We may replace the signal
-above with a new signal (with a different name) if the underlying survey item
-changes significantly.
+These indicators are based on questions added in Wave 6 of the survey,
+introduced on December 19, 2020; however, Delphi only enabled item V1 beginning
+January 6, 2021. **Note:** As of January 2021, vaccination items on the survey
+are being revised in preparation for Wave 7. We may replace the signals above
+with new signals (with different names) if the underlying survey items change
+significantly.
 
-A weighted version of this signal, using the [survey weighting described
-below](#survey-weighting) to be more representative of state demographics, is
-also available. It is `smoothed_waccept_covid_vaccine`.
+Weighted versions of these signals, using the [survey weighting described
+below](#survey-weighting) to be more representative of state demographics, are
+also available. They have names beginning with `smoothed_w`, such as
+`smoothed_waccept_covid_vaccine`.
 
 
 ## Mental Health Indicators

docs/api/covidcast.md

@@ -93,7 +93,7 @@ sources and signals.
 
 The COVIDcast API is based on HTTP GET queries and returns data in JSON form.
 The base URL is `https://api.covidcast.cmu.edu/epidata/api.php`.  The covidcast
-endpoint is `https://api.covidcast.cmu.edu/epidata/api.php?source=covidcast`.
+endpoint is `https://api.covidcast.cmu.edu/epidata/api.php?endpoint=covidcast`.
 
 See [this documentation](README.md) for details on specifying epiweeks, dates,
 and lists.
@@ -180,7 +180,7 @@ API calls.
 
 ### Facebook Survey CLI on 2020-04-06 to 2010-04-10 (county 06001)
 
-https://api.covidcast.cmu.edu/epidata/api.php?source=covidcast&data_source=fb-survey&signal=smoothed_cli&time_type=day&geo_type=county&time_values=20200406-20200410&geo_value=06001
+https://api.covidcast.cmu.edu/epidata/api.php?endpoint=covidcast&data_source=fb-survey&signal=smoothed_cli&time_type=day&geo_type=county&time_values=20200406-20200410&geo_value=06001
 
 ```json
 {
@@ -202,7 +202,7 @@ https://api.covidcast.cmu.edu/epidata/api.php?source=covidcast&data_source=fb-su
 
 ### Facebook Survey CLI on 2020-04-06 (all counties)
 
-https://api.covidcast.cmu.edu/epidata/api.php?source=covidcast&data_source=fb-survey&signal=smoothed_cli&time_type=day&geo_type=county&time_values=20200406&geo_value=*
+https://api.covidcast.cmu.edu/epidata/api.php?endpoint=covidcast&data_source=fb-survey&signal=smoothed_cli&time_type=day&geo_type=county&time_values=20200406&geo_value=*
 
 ```json
 {

docs/api/covidcast_geography.md

@@ -34,7 +34,7 @@ whose estimate is being reported. Estimates are available for several possible
 * `state`: The 50 states, identified by their two-digit postal abbreviation (in
   lower case). Estimates for Puerto Rico are available as state `pr`;
   Washington, D.C. is available as state `dc`.
-  * `nation`: accepted values are the ISO 3166-1 alpha-2 [country codes](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2). Currently the only nation we have data on is `us`.
+* `nation`: accepted values are the ISO 3166-1 alpha-2 [country codes](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2). Currently the only nation we have data on is `us`.
 
 Some signals are not available for all `geo_type`s since they may be reported
 by their original sources at geographic resolutions which are too coarse.

docs/api/covidcast_meta.md

@@ -6,7 +6,7 @@ nav_order: 6
 
 # COVIDcast Metadata
 
-The COVIDcast metadata endpoint (source `covidcast_meta`) provides a list of all
+The COVIDcast metadata endpoint (endpoint `covidcast_meta`) provides a list of all
 sources and signals available in the API, along with basic summary statistics
 such as the dates they are available, their minimum and maximum values, and the
 geographic levels at which they are reported.
@@ -45,7 +45,7 @@ None required.
 
 ## Example URLs
 
-https://api.covidcast.cmu.edu/epidata/api.php?source=covidcast_meta
+https://api.covidcast.cmu.edu/epidata/api.php?endpoint=covidcast_meta
 
 ```json
 {

docs/api/delphi.md

@@ -58,7 +58,7 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a
 # Example URLs
 
 ### Delphi on 2020w01 (EC)
-https://delphi.cmu.edu/epidata/api.php?source=delphi&system=ec&epiweek=202001
+https://delphi.cmu.edu/epidata/api.php?endpoint=delphi&system=ec&epiweek=202001
 
 ```json
 {