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Merge pull request #1566 from cmu-delphi/release/delphi-epidata-4.1.27
Release Delphi Epidata 4.1.27
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‎.bumpversion.cfg

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[bumpversion]
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current_version = 4.1.26
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current_version = 4.1.27
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commit = False
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tag = False
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‎.github/workflows/missing_signals.yaml

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run: python scripts/report_missing_covidcast_meta.py
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- name: Upload Missing Artifact
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if: failure()
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@v4
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with:
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name: missing_db_signals.csv
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path: missing_db_signals.csv

‎.github/workflows/performance-tests-one-time.yml

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write_float('requests_per_sec', final_line[9])
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- name: Archive results as artifacts
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: locust-output
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path: |

‎.github/workflows/performance-tests.yml

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write_float('requests_per_sec', final_line[9])
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- name: Archive results as artifacts
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: locust-output
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path: |

‎.github/workflows/release-helper.yml

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working-directory: src/client/packaging/pypi
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run: |
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python -m build --sdist --wheel
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- uses: actions/upload-artifact@v2
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- uses: actions/upload-artifact@v4
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with:
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name: delphi_epidata_py
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path: src/client/packaging/pypi/dist/*.tar.gz
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- run: npm pack
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- name: Rename to a different name
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run: for f in *.tgz; do mv "$f" "$(echo "$f" | sed s/delphi_epidata-/delphi_epidata_js-/)"; done
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- uses: actions/upload-artifact@v2
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- uses: actions/upload-artifact@v4
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with:
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name: delphi_epidata_js
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path: src/client/packaging/npm/*.tgz

‎dev/local/setup.cfg

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[metadata]
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name = Delphi Development
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version = 4.1.26
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version = 4.1.27
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[options]
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packages =

‎docs/about_delphi.md

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---
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title: About Delphi
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nav_order: 60
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has_children: false
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---
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# About The Delphi Group
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The Delphi Group's mission is to develop the theory and practice of epidemic detection, tracking and forecasting, and their use in decision making, both public and private.
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Our vision is to make this technology as useful as weather forecasting is today.
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Find out more about the Delphi Research Group on our <a href="https://delphi.cmu.edu" target="_blank">offical webpage</a>.
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Please read our <a href="https://delphi.cmu.edu/blog" target="_blank">blog</a> for additional news, findings, and musings from the team.
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‎docs/api/README.md

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---
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title: Other Endpoints (COVID-19 and Other Diseases)
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nav_order: 3
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has_children: true
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nav_order: 3
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---
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# Other Endpoints (COVID-19 and Other Diseases)
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# Related Work
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Please visit our [related works](related_work.md) page for more information.
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Please visit our [related works](../related_work.md) page for more information.

‎docs/api/api_keys.md

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---
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title: API Keys
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parent: Epidata API Intro
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nav_order: 1
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has_children: true
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---
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# Epidata API Keys
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### Using a client
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* covidcast
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* [epidatr](https://cmu-delphi.github.io/epidatr/#api-keys)
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* [epidatpy](https://cmu-delphi.github.io/epidatpy/#api-keys)
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* [delphi-epidata](https://cmu-delphi.github.io/delphi-epidata/api/client_libraries.html)
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* covidcast (deprecated in favor of `epidatr` and `epidatpy`)
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* [R client](https://cmu-delphi.github.io/covidcast/covidcastR/reference/covidcast_signal.html#api-keys-1)
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* [Python client](https://cmu-delphi.github.io/covidcast/covidcast-py/html/signals.html#covidcast.use_api_key)
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* [epidatr](https://github.com/cmu-delphi/epidatr#api-keys)
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* [delphi-epidata](https://cmu-delphi.github.io/delphi-epidata/api/client_libraries.html)
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### Via request parameter
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‎docs/api/cdc.md

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---
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title: CDC
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parent: Other Endpoints (COVID-19 and Other Diseases)
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title: <i>inactive</i> CDC
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parent: Data Sources and Signals
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grand_parent: Other Endpoints (COVID-19 and Other Diseases)
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nav_order: 2
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---
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# CDC

‎docs/api/client_libraries.md

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---
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title: Epidata API Client Libraries
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title: API Clients
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parent: Other Endpoints (COVID-19 and Other Diseases)
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---
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# Epidata API Client Libraries
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# Epidata API Clients
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To access Delphi Epidata programmatically, we recommend our client libraries:
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- R: [epidatr](https://cmu-delphi.github.io/epidatr/),
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- Python: [delphi-epidata](https://pypi.org/project/delphi-epidata/) (soon to be replaced with [epidatpy](https://github.com/cmu-delphi/epidatpy)),
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- Python: [epidatpy](https://cmu-delphi.github.io/epidatpy/) (recommended) and [delphi-epidata](https://pypi.org/project/delphi-epidata/),
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- Javascript: [delphi-epidata](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js).
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For anyone looking for COVIDCast data, please visit our [COVIDCast Libraries](covidcast_clients.md).
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For anyone looking for COVIDCast data, please visit our [COVIDCast API Client Libraries](covidcast_clients.md).
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The following samples show how to import the library and fetch Delphi's
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COVID-19 Surveillance Streams from Facebook Survey CLI for county 06001 and days
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Install [`epidatr` from CRAN](https://cran.r-project.org/package=epidatr)
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with `install.packages("epidatr")`.
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```R
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```r
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# Configure API key interactively, if needed. See
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# https://cmu-delphi.github.io/epidatr/articles/epidatr.html#api-keys for details.
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#save_api_key()
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library(epidatr)
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res <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
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data <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
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time_values = c(20200401, 20200405:20200414))
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cat(res)
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cat(data)
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```
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### Python
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The `epidatpy` package will soon be [available on PyPI as `epidatpy`](https://pypi.org/project/epidatpy/).
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Meanwhile, it can be [installed from GitHub](https://github.com/cmu-delphi/epidatpy/) with
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`pip install "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"`.
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```python
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# Configure API key, if needed.
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# https://github.com/cmu-delphi/epidatpy/blob/dev/docs/index.rst#api-keys
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from epidatpy import EpiDataContext, EpiRange
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# Create the client object.
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epidata = EpiDataContext()
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apicall = epidata.pub_covidcast(
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data_source="jhu-csse",
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signals="confirmed_cumulative_num",
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geo_type="nation",
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time_type="day",
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geo_values="us",
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time_values=EpiRange(20210405, 20210410),
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)
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print(apicall.df())
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```
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Install [`delphi-epidata` from PyPI](https://pypi.org/project/delphi-epidata/) with
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‎docs/api/covid_hosp.md

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---
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title: COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries
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parent: Other Endpoints (COVID-19 and Other Diseases)
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title: <i>inactive</i> COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries
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parent: Data Sources and Signals
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grand_parent: Other Endpoints (COVID-19 and Other Diseases)
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nav_order: 2
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# COVID-19 Hospitalization by State
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```json
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{
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"result": 1,
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"epidata": [
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"epidata":
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[
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{
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"state": "MA",
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"issue": 20201116,
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"geocoded_state": null,
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"issue": 20240503,
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"date": 20200510,
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"critical_staffing_shortage_today_yes": 0,
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"critical_staffing_shortage_today_no": 0,
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"critical_staffing_shortage_today_not_reported": 84,
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"critical_staffing_shortage_anticipated_within_week_yes": 0,
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"critical_staffing_shortage_anticipated_within_week_no": 0,
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"critical_staffing_shortage_anticipated_within_week_not_reported": 84,
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"hospital_onset_covid": 53,
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"hospital_onset_covid_coverage": 84,
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"inpatient_beds": 15691,
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"adult_icu_bed_utilization_coverage": null,
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"adult_icu_bed_utilization_numerator": null,
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"adult_icu_bed_utilization_denominator": null,
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"inpatient_beds_utilization": 0.6978504972730191,
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"percent_of_inpatients_with_covid": 0.2902550897239881,
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"inpatient_bed_covid_utilization": 0.21056656682174496,
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"deaths_covid": 48,
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"deaths_covid_coverage": 73,
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"icu_patients_confirmed_influenza": null,
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"icu_patients_confirmed_influenza_coverage": 0,
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"on_hand_supply_therapeutic_a_casirivimab_imdevimab_courses": null,
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"on_hand_supply_therapeutic_b_bamlanivimab_courses": null,
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"on_hand_supply_therapeutic_c_bamlanivimab_etesevimab_courses": null,
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"previous_day_admission_adult_covid_confirmed_18_19": null,
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"previous_day_admission_adult_covid_confirmed_18_19_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_20_29": null,
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"previous_day_admission_adult_covid_confirmed_20_29_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_30_39": null,
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"previous_day_admission_adult_covid_confirmed_30_39_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_40_49": null,
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"previous_day_admission_adult_covid_confirmed_40_49_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_50_59": null,
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"previous_day_admission_adult_covid_confirmed_50_59_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_60_69": null,
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"previous_day_admission_adult_covid_confirmed_60_69_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_70_79": null,
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"previous_day_admission_adult_covid_confirmed_70_79_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_80plus": null,
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"previous_day_admission_adult_covid_confirmed_80plus_coverage": 0,
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"previous_day_admission_adult_covid_confirmed_unknown": null,
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"previous_day_admission_adult_covid_confirmed_unknown_coverage": 0,
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"previous_day_admission_adult_covid_suspected_18_19": null,
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"previous_day_admission_adult_covid_suspected_18_19_coverage": 0,
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"previous_day_admission_adult_covid_suspected_20_29": null,
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"previous_day_admission_adult_covid_suspected_20_29_coverage": 0,
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"previous_day_admission_adult_covid_suspected_30_39": null,
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"previous_day_admission_adult_covid_suspected_30_39_coverage": 0,
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"previous_day_admission_adult_covid_suspected_40_49": null,
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"previous_day_admission_adult_covid_suspected_40_49_coverage": 0,
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"previous_day_admission_adult_covid_suspected_50_59": null,
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"previous_day_admission_adult_covid_suspected_50_59_coverage": 0,
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"previous_day_admission_adult_covid_suspected_60_69": null,
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"previous_day_admission_adult_covid_suspected_60_69_coverage": 0,
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"previous_day_admission_adult_covid_suspected_70_79": null,
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"previous_day_admission_adult_covid_suspected_70_79_coverage": 0,
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"previous_day_admission_adult_covid_suspected_80plus": null,
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"previous_day_admission_adult_covid_suspected_80plus_coverage": 0,
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"previous_day_admission_adult_covid_suspected_unknown": null,
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"previous_day_admission_adult_covid_suspected_unknown_coverage": 0,
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"previous_day_admission_influenza_confirmed": null,
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"previous_day_admission_influenza_confirmed_coverage": 0,
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"previous_day_deaths_covid_and_influenza": null,
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"previous_day_deaths_covid_and_influenza_coverage": 0,
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"previous_day_deaths_influenza": null,
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"previous_day_deaths_influenza_coverage": 0,
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"previous_week_therapeutic_a_casirivimab_imdevimab_courses_used": null,
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"previous_week_therapeutic_b_bamlanivimab_courses_used": null,
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"previous_week_therapeutic_c_bamlanivimab_etesevimab_courses_used": null,
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"total_patients_hospitalized_confirmed_influenza": null,
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"total_patients_hospitalized_confirmed_influenza_coverage": 0,
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"total_patients_hospitalized_confirmed_influenza_covid": null,
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"total_patients_hospitalized_confirmed_influenza_covid_coverage": null,
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"inpatient_beds_utilization": 0.697850497273019,
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"percent_of_inpatients_with_covid": 0.290255089723988,
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"inpatient_bed_covid_utilization": 0.210566566821745,
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"adult_icu_bed_covid_utilization": null,
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"adult_icu_bed_utilization": null
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}
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],
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"result": 1,
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"message": "success"
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}
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```
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# Code Samples
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Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R).

‎docs/api/covid_hosp_facility.md

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---
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title: COVID-19 Reported Patient Impact and Hospital Capacity by Facility
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parent: Other Endpoints (COVID-19 and Other Diseases)
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title: <i>inactive</i> COVID-19 Reported Patient Impact and Hospital Capacity by Facility
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parent: Data Sources and Signals
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grand_parent: Other Endpoints (COVID-19 and Other Diseases)
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nav_order: 2
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# COVID-19 Hospitalization by Facility

‎docs/api/covid_hosp_facility_lookup.md

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title: COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup
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parent: Other Endpoints (COVID-19 and Other Diseases)
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title: <i>inactive</i> COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup
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parent: Data Sources and Signals
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grand_parent: Other Endpoints (COVID-19 and Other Diseases)
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nav_order: 2
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# COVID-19 Hospitalization: Facility Lookup

‎docs/api/covidcast-signals/_source-template.md

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title: SOURCE NAME
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# SOURCE NAME

‎docs/api/covidcast-signals/chng.md

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title: Change Healthcare
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# Change Healthcare
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| Signal | Description |
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| --- | --- |
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| `7dav_inpatient_covid` | Ratio of inpatient hospitalizations associated with COVID-19, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time with a trailing 7 day average. This historical signal is no longer updated. <br/> **Earliest date available:** 2020-01-01 |
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| `7dav_outpatient_covid` | Ratio of outpatient doctor visits with confirmed COVID-19, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time with a trailing 7 day average. This historical signal is no longer updated. <br/> **Earliest date available:** 2020-01-01 |
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| `smoothed_outpatient_covid` | Estimated percentage of outpatient doctor visits with confirmed COVID-19, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time using a Gaussian linear smoother <br/> **Earliest date available:** 2020-02-01 |
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| `smoothed_adj_outpatient_covid` | Same, but with systematic day-of-week effects removed; see [details below](#day-of-week-adjustment) <br/> **Earliest date available:** 2020-02-01 |
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| `smoothed_outpatient_cli` | Estimated percentage of outpatient doctor visits primarily about COVID-related symptoms, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time using a Gaussian linear smoother <br/> **Earliest date available:** 2020-02-01 |

‎docs/api/covidcast-signals/covid-act-now.md

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title: <i>inactive</i> COVID Act Now
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parent: Data Sources and Signals
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grand_parent: Main Endpoint (COVIDcast)
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nav_order: 2
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# COVID Act Now (CAN)

‎docs/api/covidcast-signals/doctor-visits.md

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# Doctor Visits

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

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title: Data Strategy and Execution Workgroup Community Profile Report
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grand_parent: COVIDcast Main Endpoint
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title: <i>inactive</i> Data Strategy and Execution Workgroup Community Profile Report
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parent: Data Sources and Signals
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grand_parent: Main Endpoint (COVIDcast)
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# Data Strategy and Execution Workgroup Community Profile Report (CPR)

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