Merge branch 'dev' into nsspDocs

Author: nmdefries

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.20
+current_version = 4.1.23
 commit = False
 tag = False
 
@@ -9,10 +9,10 @@ tag = False
 
 [bumpversion:file:src/client/delphi_epidata.R]
 
+[bumpversion:file:src/client/delphi_epidata.py]
+
 [bumpversion:file:src/client/packaging/npm/package.json]
 
 [bumpversion:file:src/client/packaging/pypi/setup.py]
 
-[bumpversion:file:src/client/packaging/pypi/delphi_epidata/__init__.py]
-
 [bumpversion:file:dev/local/setup.cfg]

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.20
+version = 4.1.23
 
 [options]
 packages =

docs/Gemfile.lock

@@ -225,7 +225,8 @@ GEM
     rb-fsevent (0.10.4)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.2.5)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rouge (3.26.0)
     ruby-enum (0.9.0)
       i18n
@@ -242,6 +243,7 @@ GEM
       faraday (> 0.8, < 2.0)
     simpleidn (0.2.1)
       unf (~> 0.1.4)
+    strscan (3.1.0)
     terminal-table (1.8.0)
       unicode-display_width (~> 1.1, >= 1.1.1)
     thread_safe (0.3.6)

docs/api/client_libraries.md

@@ -6,69 +6,81 @@ nav_order: 1
 
 # Epidata API Client Libraries
 
-For anyone looking for COVIDCast data, please visit our [COVIDCast Libraries](covidcast_clients.md).
+To access Delphi Epidata programmatically, we recommend our client libraries:
 
-We are currently working on fully-featured Epidata clients for R and Python. They are not ready
-for release yet, but you can track our development progress and help us test them out at:
+- R: [epidatr](https://cmu-delphi.github.io/epidatr/),
+- 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).
 
-* [epidatr](https://github.com/cmu-delphi/epidatr)
-* [epidatpy](https://github.com/cmu-delphi/epidatpy)
+For anyone looking for COVIDCast data, please visit our [COVIDCast Libraries](covidcast_clients.md).
 
-In the meantime, minimalist Epidata clients remain available for
-[JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js),
-[Python](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.py),
-and
-[R](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.R).
-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
+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
 `20200401` and `20200405-20200414` (11 days total).
 
-### JavaScript (in a web browser)
+### R
 
-The minimalist JavaScript client does not currently support API keys. If you need API key support in JavaScript, contact [email protected].
+Install [`epidatr` from CRAN](https://cran.r-project.org/package=epidatr)
+with `install.packages("epidatr")`.
 
-````html
-<!-- Imports -->
-<script src="delphi_epidata.js"></script>
-<!-- Fetch data -->
-<script>
-  EpidataAsync.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401, EpidataAsync.range(20200405, 20200414)], '06001').then((res) => {
-    console.log(res.result, res.message, res.epidata != null ? res.epidata.length : 0);
-  });
-</script>
-````
+```R
+# Configure API key interactively, if needed. See
+# https://cmu-delphi.github.io/epidatr/articles/epidatr.html#api-keys for details.
+#save_api_key()
+library(epidatr)
+res <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
+                     time_values = c(20200401, 20200405:20200414))
+cat(res)
+```
 
 ### Python
 
+Install [`delphi-epidata` from PyPI](https://pypi.org/project/delphi-epidata/) with
+`pip install delphi-epidata`.
 
-Optionally install the [package from PyPI](https://pypi.org/project/delphi-epidata/) using pip(env):
-````bash
-pip install delphi-epidata
-````
-
-Otherwise, place
-[`delphi_epidata.py`](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.py)
-in the same directory as your Python script.
-
-````python
-# Import
+```python
 from delphi_epidata import Epidata
-# [Optional] configure your API key, if desired
+# Configure API key, if needed.
 #Epidata.auth = ('epidata', <your API key>)
-# Fetch data
 res = Epidata.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401, Epidata.range(20200405, 20200414)], '06001')
 print(res['result'], res['message'], len(res['epidata']))
-````
+```
 
-### R
+### JavaScript (in a web browser)
+
+The minimalist JavaScript client does not currently support API keys.
+If you need API key support in JavaScript, contact [email protected].
+
+```html
+<script src="delphi_epidata.js"></script>
+<script>
+  EpidataAsync.covidcast(
+    "fb-survey",
+    "smoothed_cli",
+    "day",
+    "county",
+    [20200401, EpidataAsync.range(20200405, 20200414)],
+    "06001"
+  ).then((res) => {
+    console.log(
+      res.result,
+      res.message,
+      res.epidata != null ? res.epidata.length : 0
+    );
+  });
+</script>
+```
+
+### R (legacy)
 
+The old Delphi Epidata R client is available
+[here](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R),
+but its use is discouraged.
 
-````R
-# [Optional] configure your API key, if desired
+```R
+# Configure API key, if needed.
 #option('epidata.auth', <your API key>)
-# Import
 source('delphi_epidata.R')
-# Fetch data
 res <- Epidata$covidcast('fb-survey', 'smoothed_cli', 'day', 'county', list(20200401, Epidata$range(20200405, 20200414)), '06001')
 cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+```

docs/api/covidcast_clients.md

@@ -6,15 +6,15 @@ nav_order: 1
 
 # COVIDcast Libraries
 
-Dedicated COVIDcast access and analysis libraries are available for several languages:
+To access COVIDcast data, we recommend using the following client libraries:
 
-* R: [covidcast](https://cmu-delphi.github.io/covidcast/covidcastR/)
-* Python: [covidcast](https://cmu-delphi.github.io/covidcast/covidcast-py/html/)
+- 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 functions. For installation instructions and examples, consult their
-respective webpages.
+ready to be used in further analyses and provide convenient mapping and analysis
+functions. For installation instructions and examples, consult their respective
+webpages.
 
-
-To access Epidata datasets on other diseases, visit our [Epidata API Client Libraries)](client_libraries.md) documentation.
+To access Epidata datasets on other diseases, visit our
+[Epidata API Client Libraries](client_libraries.md) documentation.

docs/symptom-survey/publications.md

@@ -26,6 +26,18 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*:
 
 Research publications using the survey data include:
 
+- Y. Yang, W. Dempsey, P. Han, Y. Deshmukh, S. Richardson, B. Tom, and B. Mukherjee
+  (2024). [Exploring the Big Data Paradox for various estimands using vaccination
+  data from the global COVID-19 Trends and Impact Survey (CTIS)](https://doi.org/10.1126/sciadv.adj0266).
+  *Science Advances* 10 (22).
+- Perofsky, A.C., Hansen, C.L., Burstein, R. et al (2024). [Impacts of human
+  mobility on the citywide transmission dynamics of 18 respiratory viruses
+  in pre- and post-COVID-19 pandemic years](https://doi.org/10.1038/s41467-024-48528-2).
+  *Nature Communications* 15, 4164.
+- Z. Yang, R. Krishnan, and B. Li (2024). [The interplay between individual
+  mobility, health risk, and economic choice: A holistic model for COVID-19
+  policy intervention](https://doi.org/10.1287/ijds.2023.0013). *INFORMS
+  Journal on Data Science*.
 - A. Srivastava, J. M. Ramirez, S. Díaz-Aranda, J. Aguilar, A. F. Anta, A. Ortega,
   and R. E. Lillo (2024). [Nowcasting temporal trends using indirect surveys](https://doi.org/10.1609/aaai.v38i20.30242).
   In *Proceedings of the 38th AAAI Conference on Artificial Intelligence* 38,

requirements.api.txt

@@ -1,4 +1,4 @@
-delphi_utils==0.3.15
+delphi_utils
 epiweeks==2.1.2
 Flask==2.2.5
 Flask-Limiter==3.3.0
@@ -10,7 +10,7 @@ pandas==1.2.3
 python-dotenv==0.15.0
 pyyaml
 redis==3.5.3
-requests==2.31.0
+requests==2.32.0
 scipy==1.10.0
 sentry-sdk[flask]
 SQLAlchemy==1.4.40

requirements.dev.txt

@@ -2,7 +2,7 @@ aiohttp==3.9.4
 black>=20.8b1
 bump2version==1.0.1
 covidcast==0.1.5
-delphi_utils==0.3.15
+delphi_utils
 docker==6.0.1
 dropbox==11.36.0
 freezegun==1.2.2
@@ -13,7 +13,6 @@ mypy>=0.790
 mysql-connector==2.2.9
 numpy==1.22.4
 pycountry==22.3.5
-pymysql==1.0.2
 pytest==7.2.0
 pytest-check==1.3.0
 sas7bdat==2.2.3