+
+```json
+{
+ "result": 1,
+ "epidata": [
+ {
+ "location": "nat",
+ "epiweek": 201501,
+ "num1": 91858,
+ "num2": 81121,
+ "num3": 89511,
+ "num4": 52278,
+ "num5": 16219,
+ "num6": 87327,
+ "num7": 38310,
+ "num8": 51461,
+ "total": 4252190,
+ "value": null
+ }
+ ],
+ "message": "success"
+}
+```
# Code Samples
-
+Libraries are available for [R](https://cmu-delphi.github.io/epidatr/) and [Python](https://cmu-delphi.github.io/epidatpy/).
+The following samples show how to import the library and fetch CDC data for national level for epiweek `201501`.
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pvt_cdc(auth='auth_token', locations=['nat'], epiweeks=[201501])
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_cdc(auth = 'auth_token', locations = 'nat', epiweeks = 201501)
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.cdc('auth_token', [201501], ['nat'])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$cdc(auth = "auth_token", epiweeks = list(201501), locations = list("nat"))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+You can install the stable version of `epidatr` from CRAN:
```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)
-data <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
- time_values = c(20200401, 20200405:20200414))
-cat(data)
+install.packages("epidatr")
+# Or use pak/renv
+pak::pkg_install("epidatr")
```
+If you want the development version, install from GitHub:
-### Python
+```r
+remotes::install_github("cmu-delphi/epidatr", ref = "dev")
+```
+
+
+
The `epidatpy` package will soon be [available on PyPI as `epidatpy`](https://pypi.org/project/epidatpy/).
Meanwhile, it can be [installed from GitHub](https://github.com/cmu-delphi/epidatpy/) with
-`pip install "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"`.
+
+```Python
+pip install "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+
+
+
+
+
+
+```r
+library(epidatr)
+library(dplyr)
+
+# Obtain the most up-to-date version of the smoothed covid-like illness (CLI)
+# signal from the COVID-19 Trends and Impact survey for the US
+epidata <- pub_covidcast(
+ source = "fb-survey",
+ signals = "smoothed_cli",
+ geo_type = "nation",
+ time_type = "day",
+ geo_values = "us",
+ time_values = epirange(20210105, 20210410)
+)
+head(epidata)
+```
+
+
+
```python
-# Configure API key, if needed.
-# https://github.com/cmu-delphi/epidatpy/blob/dev/docs/index.rst#api-keys
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
-from epidatpy import EpiDataContext, EpiRange
+# Initialize client (caching enabled for 7 days)
+epidata = EpiDataContext(use_cache=True, cache_max_age_days=7)
-# Create the client object.
-epidata = EpiDataContext()
+# Obtain the most up-to-date version of the confirmed cumulative cases
+# from JHU CSSE for the US
apicall = epidata.pub_covidcast(
data_source="jhu-csse",
signals="confirmed_cumulative_num",
@@ -55,9 +116,352 @@ apicall = epidata.pub_covidcast(
geo_values="us",
time_values=EpiRange(20210405, 20210410),
)
-print(apicall.df())
+print(apicall.df().head())
```
+
+
+
+
+
+
+```r
+# Obtain data for all states
+pub_covidcast(
+ source = "fb-survey",
+ signals = "smoothed_cli",
+ geo_type = "state",
+ time_type = "day",
+ geo_values = "*",
+ time_values = epirange(20210105, 20210410)
+)
+```
+
+
+
+
+```python
+# Obtain data for all states
+epidata.pub_covidcast(
+ data_source="fb-survey",
+ signals="smoothed_cli",
+ geo_type="state",
+ time_type="day",
+ geo_values="*",
+ time_values=EpiRange(20210405, 20210410),
+).df()
+```
+
+
+
+
+
+
+
+```r
+# Obtain data for PA, CA, and FL
+pub_covidcast(
+ source = "fb-survey",
+ signals = "smoothed_cli",
+ geo_type = "state",
+ time_type = "day",
+ geo_values = c("pa", "ca", "fl"),
+ time_values = "*"
+)
+```
+
+
+
+
+```python
+# Obtain data for PA, CA, and FL
+epidata.pub_covidcast(
+ data_source="fb-survey",
+ signals="smoothed_cli",
+ geo_type="state",
+ time_type="day",
+ geo_values="pa,ca,fl",
+ time_values="*",
+).df()
+```
+
+
+
+
+
+
+
+```r
+# Obtain the signal as it was on 2021-06-01
+pub_covidcast(
+ source = "fb-survey",
+ signals = "smoothed_cli",
+ geo_type = "state",
+ time_type = "day",
+ geo_values = "pa",
+ time_values = epirange(20210105, 20210410),
+ as_of = "2021-06-01"
+)
+```
+
+
+
+
+```python
+# Obtain the signal as it was on 2021-06-01
+epidata.pub_covidcast(
+ data_source="fb-survey",
+ signals="smoothed_cli",
+ geo_type="state",
+ time_type="day",
+ geo_values="pa",
+ time_values=EpiRange(20210405, 20210410),
+ as_of="2021-06-01",
+).df()
+```
+
+
+
+
+
+
+
+```r
+# See how the estimate for a SINGLE day (March 1, 2021) evolved
+# by fetching all issues reported between March and April 2021.
+pub_covidcast(
+ source = "fb-survey",
+ signals = "smoothed_cli",
+ geo_type = "state",
+ time_type = "day",
+ geo_values = "pa",
+ time_values = "2021-03-01",
+ issues = epirange("2021-03-01", "2021-04-30")
+)
+```
+
+
+
+
+```python
+# See how the estimate for a SINGLE day (March 1, 2021) evolved
+# by fetching all issues reported between March and April 2021.
+epidata.pub_covidcast(
+ data_source="fb-survey",
+ signals="smoothed_cli",
+ geo_type="state",
+ time_type="day",
+ geo_values="pa",
+ time_values="2021-03-01",
+ issues=EpiRange("2021-03-01", "2021-04-30"),
+).df()
+```
+
+
+
+
+
+
+
+```r
+# Fetch survey data for January 2021, but ONLY include data
+# that was issued exactly 2 days after it was collected.
+pub_covidcast(
+ source = "fb-survey",
+ signals = "smoothed_cli",
+ geo_type = "state",
+ time_type = "day",
+ geo_values = "pa",
+ time_values = epirange(20210101, 20210131),
+ lag = 2
+)
+```
+
+
+
+
+```python
+# Fetch survey data for January 2021, but ONLY include data
+# that was issued exactly 2 days after it was collected.
+epidata.pub_covidcast(
+ data_source="fb-survey",
+ signals="smoothed_cli",
+ geo_type="state",
+ time_type="day",
+ geo_values="pa",
+ time_values=EpiRange(20210101, 20210131),
+ lag=2,
+).df()
+```
+
+
+
+
+
+
+
+```r
+library(ggplot2)
+ggplot(epidata, aes(x = time_value, y = value)) +
+ geom_line() +
+ labs(
+ title = "Smoothed CLI from Facebook Survey",
+ subtitle = "PA, 2021",
+ x = "Date",
+ y = "CLI"
+ )
+```
+
+
+
+
+```python
+import matplotlib.pyplot as plt
+
+# Fetch data for PA, CA, FL
+apicall = epidata.pub_covidcast(
+ data_source="fb-survey",
+ signals="smoothed_cli",
+ geo_type="state",
+ geo_values="pa,ca,fl",
+ time_type="day",
+ time_values=EpiRange(20210405, 20210410),
+)
+
+# Plot
+fig, ax = plt.subplots(figsize=(6, 5))
+(
+ apicall.df()
+ .pivot_table(values="value", index="time_value", columns="geo_value")
+ .plot(xlabel="Date", ylabel="CLI", ax=ax, linewidth=1.5)
+)
+plt.title("Smoothed CLI from Facebook Survey")
+plt.show()
+```
+
+
+
+
+
+
+
+```r
+# Get a table of endpoint functions
+avail_endpoints()
+```
+
+
+
+
+```python
+# List sources available in the pub_covidcast endpoint
+covidcast = CovidcastEpidata(use_cache=True)
+print(covidcast.source_names())
+
+# List signals available for a specific source (e.g., jhu-csse)
+print(covidcast.signal_names("jhu-csse"))
+```
+
+
+
+
+
+
+
Install [`delphi-epidata` from PyPI](https://pypi.org/project/delphi-epidata/) with
`pip install delphi-epidata`.
@@ -68,8 +472,21 @@ from delphi_epidata import Epidata
res = Epidata.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401, Epidata.range(20200405, 20200414)], '06001')
print(res['result'], res['message'], len(res['epidata']))
```
+
-### JavaScript (in a web browser)
+
+
+
+```R
+# Configure API key, if needed.
+#option('epidata.auth', )
+source('delphi_epidata.R')
+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"))
+```
+
+
+
The minimalist JavaScript client does not currently support API keys.
If you need API key support in JavaScript, contact delphi-support+privacy@andrew.cmu.edu.
@@ -77,33 +494,23 @@ If you need API key support in JavaScript, contact delphi-support+privacy@andrew
```html
-```
-
-### 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.
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_covid_hosp(states="MA", dates=20200510)
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_covid_hosp_state_timeseries(states = "MA", dates = 20200510)
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
```bash
@@ -260,3 +308,19 @@ The following issues were repaired:
These issues had been imported using the wrong column order due to an imprecise
database migration. If you pulled these issues before January 22, you will want
to discard that data.
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$covid_hosp(states = list("MA"), dates = list(20200510))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_covid_hosp_facility(hospital_pks="390119", collection_weeks=EpiRange(20201201, 20201207))
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_covid_hosp_facility(hospital_pks = "390119", collection_weeks = epirange(20201201, 20201207))
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
res = Epidata.covid_hosp_facility('390119', Epidata.range(20201201, 20201207))
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$covid_hosp_facility(hospital_pks = list("390119"), collection_weeks = list(Epidata$range(20201201, 20201207)))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_covid_hosp_facility_lookup(city="southlake")
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_covid_hosp_facility_lookup(city = "southlake")
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
res = Epidata.covid_hosp_facility_lookup(city='southlake')
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$covid_hosp_facility_lookup(city = "southlake")
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+Click to expand
+
+Your collapsible content goes here. You can still use **Markdown** inside.
+
+
+
## Table of contents
{: .no_toc .text-delta}
diff --git a/docs/api/covidcast-signals/chng.md b/docs/api/covidcast-signals/chng.md
index 06b6d5a29..b5e7561f1 100644
--- a/docs/api/covidcast-signals/chng.md
+++ b/docs/api/covidcast-signals/chng.md
@@ -1,24 +1,36 @@
---
-title: Change Healthcare
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 1
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
+title: inactive Change Healthcare
---
# Change Healthcare
{: .no_toc}
-* **Source name:** `chng`
-* **Earliest issue available:** November 4, 2020
-* **Number of data revisions since May 19, 2020:** 0
-* **Date of last change:** Never
-* **Available for:** county, hrr, msa, state, hhs, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** [CC BY-NC](../covidcast_licensing.md#creative-commons-attribution-noncommercial)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `chng` |
+| **Data Source** | Change Healthcare |
+| **Geographic Levels** | National, U.S. HHS Region, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2024-02-19 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-02-01 |
+| **License** | [CC BY-NC](../covidcast_licensing.md#creative-commons-attribution-noncommercial) |
-## Overview
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
-**Notice: This data source was inactive between 2021-10-04 and 2021-12-02 to allow us resolve some problems with the data pipeline. We have resumed daily updates and are working on a data patch to fill the gap. [Additional details on this inactive period are available below](#pipeline-pause).**
+
+
+## Overview
+{: .no_toc}
This data source is based on Change Healthcare claims data that has been
de-identified in accordance with HIPAA privacy regulations. Change Healthcare is
diff --git a/docs/api/covidcast-signals/covid-act-now.md b/docs/api/covidcast-signals/covid-act-now.md
index 41a5cabc2..d6420627e 100644
--- a/docs/api/covidcast-signals/covid-act-now.md
+++ b/docs/api/covidcast-signals/covid-act-now.md
@@ -1,20 +1,35 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive COVID Act Now
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# COVID Act Now (CAN)
{: .no_toc}
-* **Source name:** `covid-act-now`
-* **Earliest issue available:** 2021-03-25
-* **Number of data revisions since 19 May 2020:** 0
-* **Date of last change:** Never
-* **Available for:** county, hrr, msa, state, hhs, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** [CC BY-NC](../covidcast_licensing.md#creative-commons-attribution-noncommercial)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `covid-act-now` |
+| **Data Source** | COVID Act Now |
+| **Geographic Levels** | National, U.S. HHS Region, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2021-12-02 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-03-01 |
+| **License** | [CC BY-NC](../covidcast_licensing.md#creative-commons-attribution-noncommercial) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
+
+## Overview
The [COVID Act Now (CAN)](https://covidactnow.org/) data source provides COVID-19 testing statistics, such as positivity rates and total tests performed.
The county-level positivity rates and test totals are pulled directly from CAN using [their API](https://covidactnow.org/data-api).
diff --git a/docs/api/covidcast-signals/covid-trends-and-impact-survey.md b/docs/api/covidcast-signals/covid-trends-and-impact-survey.md
index 147566f98..69f354de9 100644
--- a/docs/api/covidcast-signals/covid-trends-and-impact-survey.md
+++ b/docs/api/covidcast-signals/covid-trends-and-impact-survey.md
@@ -1,21 +1,53 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive 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 (CTIS)
{: .no_toc}
-* **Source name:** `fb-survey`
-* **Earliest issue available:** April 29, 2020
-* **Number of data revisions since May 19, 2020:** 1
-* **Date of last change:** [June 3, 2020](../covidcast_changelog.md#fb-survey)
-* **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)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `fb-survey` |
+| **Data Source** | [COVID-19 Trends and Impact Survey (CTIS)](../../symptom-survey/) |
+| **Geographic Levels** | National, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2022-06-25 |
+| **Date of last data revision:** | June 3, 2020 (see [data revision docs](../covidcast_changelog.md#fb-survey)) |
+| **Temporal Scope Start** | Varies by indicator - 2020-2021 |
+| **License** | [CC BY](../covidcast_licensing.md#creative-commons-attribution) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+### June 3, 2020
+
+Duplicate survey weights had corrupted historical figures for the following signals and dates. The correct data has been restored to the API.
+* `raw_wcli`
+ * `county`: 20200406, 20200408, 20200410, 20200430
+ * `hrr`: 20200406, 20200408-20200410, 20200430
+ * `msa`: 20200408, 20200410, 20200430
+ * `state`: 20200408-20200410, 20200430
+* `smoothed_wcli`
+ * `county`: 20200406, 20200408-20200414, 20200430-20200506
+ * `hrr`: 20200406-20200415, 20200430-20200506
+ * `msa`: 20200408-20200414, 20200430-20200506
+ * `state`: 20200408-20200416, 20200430-20200506
+
+### November 20, 2020
+
+Due to a bug in our data processing system, estimates of the percentage of people reporting that they have been tested for COVID-19 calculated before October 8th were incorrect.
+We incorrectly treated an answer of “no” as a missing response, which affected the `smoothed_tested_14d` and `smoothed_wtested_14d` signals from the `fb-survey` source.
+
+As of Nov. 20th, the error has been corrected and all affected data reissued.
+
+
## Overview
@@ -790,12 +822,11 @@ of zero, and in simulations improves the quality of the standard error
estimates. See the [Appendix](#appendix) for further motivation for these
estimators.
-Note:
-Currently the standard errors are calculated as though all survey weights are
-equal, that is \(w^\text{part}_i = 1\) for all respondents. The result is that
-reported standard errors are artificially narrow for weighted estimates. This
-will be corrected in a future update to the API.
-
+> **Note:** Currently the standard errors are calculated as though all survey weights are
+> equal, that is $$w^\text{part}_i = 1$$ for all respondents. The result is that
+> reported standard errors are artificially narrow for weighted estimates. This
+> will be corrected in a future update to the API.
+{: .note }
The pseudo-observation is not used in $$\hat{p}$$ and $$\hat{q}$$ themselves, to
avoid potentially large amounts of estimation bias, as $$p$$ and $$q$$ are
diff --git a/docs/api/covidcast-signals/doctor-visits.md b/docs/api/covidcast-signals/doctor-visits.md
index 5eb9c96a9..6ce2d3071 100644
--- a/docs/api/covidcast-signals/doctor-visits.md
+++ b/docs/api/covidcast-signals/doctor-visits.md
@@ -8,16 +8,31 @@ nav_order: 1
# Doctor Visits
{: .no_toc}
-* **Source name:** `doctor-visits`
-* **Earliest issue available:** April 29, 2020
-* **Number of data revisions since May 19, 2020:** 1
-* **Date of last change:** November 9, 2020
-* **Available for:** county, hrr, msa, state (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)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `doctor-visits` |
+| **Data Source** | Health system partners |
+| **Geographic Levels** | State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Daily |
+| **Date of last data revision:** | November 9, 2020 (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-02-01 |
+| **License** | [CC BY](../covidcast_licensing.md#creative-commons-attribution) |
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+### November 9, 2020
+We went from a custom geo-mapping file (for aggregating from county->(msa, hrr, state)) to a central geo file based on rigorously sourced US census data.
+
+
## Overview
+{: .no_toc}
This data source is based on information about outpatient visits, provided to us
by health system partners. Using this outpatient data, we estimate the
@@ -50,15 +65,12 @@ $$
Y_{it}^{\text{Flu}}\right)}{N_{it}}
$$
-The estimated standard error is:
+**Note on Uncertainty:** The standard error formula below represents the theoretical error of the binomial proportion. However, due to the smoothing and day-of-week adjustments applied later in the pipeline, the actual standard error in the final signal will differ.
$$
\widehat{\text{se}}(\hat{p}_{it}) = 100 \sqrt{\frac{\frac{\hat{p}_{it}}{100}(1-\frac{\hat{p}_{it}}{100})}{N_{it}}}.
$$
-Note the quantity above is not going to be correct for multiple reasons: smoothing/day of
-week adjustments/etc.
-
### Day-of-Week Adjustment
The fraction of visits due to CLI is dependent on the day of the week. On
diff --git a/docs/api/covidcast-signals/dsew-cpr.md b/docs/api/covidcast-signals/dsew-cpr.md
index 82e76d7df..fa6887581 100644
--- a/docs/api/covidcast-signals/dsew-cpr.md
+++ b/docs/api/covidcast-signals/dsew-cpr.md
@@ -1,20 +1,35 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive Data Strategy and Execution Workgroup Community Profile Report
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# Data Strategy and Execution Workgroup Community Profile Report (CPR)
{: .no_toc}
-* **Source name:** `dsew-cpr`
-* **Earliest issue available:** 2022-01-28
-* **Number of data revisions since 19 May 2020:** 0
-* **Date of last change:** Never
-* **Available for:** county, msa, state, hhs, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** [Public Domain US Government](https://www.usa.gov/government-works)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `dsew-cpr` |
+| **Data Source** | [Community Profile Report (CPR)](https://healthdata.gov/Health/COVID-19-Community-Profile-Report/gqxm-d9w9) |
+| **Geographic Levels** | National, U.S. HHS Region, State, County, Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2023-02-22 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | Varies by indicator - 2020-2021 |
+| **License** | [Public Domain US Government](https://www.usa.gov/government-works) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
+
+## Overview
The Community Profile Report (CPR) is published by the Data Strategy and Execution Workgroup (DSEW) of the White House COVID-19 Team. For more information, see the [official description at healthdata.gov](https://healthdata.gov/Health/COVID-19-Community-Profile-Report/gqxm-d9w9) for "COVID-19 Community Profile Report". Each issue of the CPR is made available as an attachment on that page. You can view all attachments by scrolling to the bottom of the "About this dataset" panel and clicking "Show more".
diff --git a/docs/api/covidcast-signals/ght.md b/docs/api/covidcast-signals/ght.md
index 9b592f60e..612434016 100644
--- a/docs/api/covidcast-signals/ght.md
+++ b/docs/api/covidcast-signals/ght.md
@@ -1,19 +1,33 @@
---
-title: inactive Google Health Trends
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
+title: inactive (COVIDcast) Google Health Trends
---
# Google Health Trends
{: .no_toc}
-* **Source name:** `ght`
-* **Earliest issue available:** April 29, 2020
-* **Number of data revisions since May 19, 2020:** 0
-* **Date of last change:** Never
-* **Available for:** dma, hrr, msa, state (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `ght` |
+| **Data Source** | Google Health Trends |
+| **Geographic Levels** | State, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA), Designated Marketing Area (DMA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2021-03-04 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-02-01 |
+| **License** | [Google Terms of Service](https://policies.google.com/terms)|
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
## Overview
diff --git a/docs/api/covidcast-signals/google-survey.md b/docs/api/covidcast-signals/google-survey.md
index d758d6a8b..701182447 100644
--- a/docs/api/covidcast-signals/google-survey.md
+++ b/docs/api/covidcast-signals/google-survey.md
@@ -1,20 +1,33 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive Google Symptom Surveys
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# Google Symptom Surveys
{: .no_toc}
-* **Source name:** `google-survey`
-* **Earliest issue available:** May 01, 2020
-* **Number of data revisions since May 19, 2020:** 0
-* **Date of last change:** Never
-* **Available for:** county, hrr, msa, state (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)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `google-survey` |
+| **Data Source** | [Google-run symptom surveys](https://9to5google.com/2020/03/23/google-coronavirus-survey/)/Delphi |
+| **Geographic Levels** | National, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2020-05-14 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-04-11 |
+| **License** | [CC BY](../covidcast_licensing.md#creative-commons-attribution) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
## Overview
@@ -26,7 +39,7 @@ is sick (fever, along with cough, or shortness of breath, or difficulty
breathing) right now?" Using this survey data, we estimate the percentage of
people in a given location, on a given day, that *know somebody who has a
COVID-like illness*. This estimates a similar quantity to the `*_cmnty_cli`
-signals from the [COVID-19 Trends and Impact Survey](fb-survey.md) (`fb-survey`) source, but using
+signals from the [COVID-19 Trends and Impact Survey](covid-trends-and-impact-survey.md) (`fb-survey`) source, but using
a different survey population and recruitment method.
The survey sampled from all counties with greater than 100,000 population, along
diff --git a/docs/api/covidcast-signals/google-symptoms.md b/docs/api/covidcast-signals/google-symptoms.md
index f37926242..64b6e3a7d 100644
--- a/docs/api/covidcast-signals/google-symptoms.md
+++ b/docs/api/covidcast-signals/google-symptoms.md
@@ -1,22 +1,40 @@
---
-title: Google Symptom Search Trends
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 1
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
+title: inactive Google Symptom Search Trends
---
# Google Symptoms
{: .no_toc}
-* **Source name:** `google-symptoms`
-* **Earliest issue available:** Aug 20, 2017
-* **Number of data revisions since May 19, 2020:** 1
-* **Date of last change:** February 28, 2025
-* **Available for:** county, MSA, HRR, state, HHS, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** To download or use the data, you must agree to the Google [Terms of Service](https://policies.google.com/terms)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `google-symptoms` |
+| **Data Source** | Google |
+| **Geographic Levels** | National, U.S. HHS Region, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated after November 16th, 2025 |
+| **Date of last data revision:** | March 14th, 2025 (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | February 13th, 2020, with some variation depending on geographic area|
+| **License** | [Google Terms of Service](https://policies.google.com/terms) |
+
+## Changelog
+
+
+Click to expand
+
+
+### March 14, 2025
+Google made earlier data available (back to August 15, 2017), and fixed a gap in county-level data between November 14, 2022 and February 20, 2023.
+
+### February 14, 2025
+Two new signals were added, relating to conjunctivitis: `s07_raw_search` and `s07_smoothed_search`.
+
+
+
## Overview
+{: .no_toc}
This data source is based on the [COVID-19 Search Trends symptoms
dataset](https://console.cloud.google.com/marketplace/product/bigquery-public-datasets/covid19-search-trends?hl=en-GB).
diff --git a/docs/api/covidcast-signals/hhs.md b/docs/api/covidcast-signals/hhs.md
index d591aa720..a7d336a43 100644
--- a/docs/api/covidcast-signals/hhs.md
+++ b/docs/api/covidcast-signals/hhs.md
@@ -1,20 +1,35 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive HHS Hospitalizations from NHSN
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# Department of Health & Human Services Hospitalizations
{: .no_toc}
-* **Source name:** `hhs`
-* **Earliest issue available:** November 16, 2020
-* **Number of data revisions since 19 May 2020:** 0
-* **Date of last change:** Never
-* **Available for:** state, hhs, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** [Public Domain US Government](https://www.usa.gov/government-works)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `hhs` |
+| **Data Source** | U.S. Department of Health & Human Services |
+| **Geographic Levels** | National, U.S. HHS Region, State (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - no longer updated since 2024-04-30 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2019-12-31 |
+| **License** | [Public Domain US Government](https://www.usa.gov/government-works) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
+
+## Overview
The U.S. Department of Health & Human Services (HHS) publishes several
datasets on patient impact and hospital capacity. The data is made available
@@ -34,20 +49,24 @@ adult and pediatric COVID-19 hospital admissions. This sum is used as the
We also include influenza hospital admissions.
-| Signal and 7-day average signal | Description |
-|---|---|
-| `confirmed_admissions_covid_1d` and `confirmed_admissions_covid_1d_7dav` | Sum of adult and pediatric confirmed COVID-19 hospital admissions occurring each day.
**Earliest date available:** 2019-12-31 |
-| `confirmed_admissions_covid_1d_prop` and `confirmed_admissions_covid_1d_prop_7dav` | Sum of adult and pediatric confirmed COVID-19 hospital admissions occurring each day, per 100,000 population.
**Earliest date available:** 2019-12-31 |
-| `sum_confirmed_suspected_admissions_covid_1d` and `sum_confirmed_suspected_admissions_covid_1d_7dav` | Sum of adult and pediatric confirmed and suspected COVID-19 hospital admissions occurring each day.
**Earliest date available:** 2019-12-31 |
-| `sum_confirmed_suspected_admissions_covid_1d_prop` and
`sum_confirmed_suspected_admissions_covid_1d_prop_7dav` | Sum of adult and pediatric confirmed and suspected COVID-19 hospital admissions occurring each day, per 100,000 population.
**Earliest date available:** 2019-12-31 |
-| `confirmed_admissions_influenza_1d` and `confirmed_admissions_influenza_1d_7dav` | All confirmed influenza hospital admissions occurring each day. We made this signal available November 1, 2021.
**Earliest issue available:** 2021-09-20
**Earliest date available:** 2020-01-02 |
-| `confirmed_admissions_influenza_1d_prop` and `confirmed_admissions_influenza_1d_prop_7dav` | All confirmed influenza hospital admissions occurring each day, per 100,000 population. We made this signal available November 1, 2021.
**Earliest issue available:** 2021-09-20
**Earliest date available:** 2020-01-02 |
+Each metric below is available in four variants:
+1. **Raw Count:** `_1d`
+2. **Smoothed (7-day average):** `_1d_7dav`
+3. **Population Proportion (per 100k):** `_1d_prop`
+4. **Smoothed Proportion:** `_1d_prop_7dav`
+
+| Metric | Base Signal Name | Description |
+| :--- | :--- | :--- |
+| **Confirmed COVID-19** | `confirmed_admissions_covid` | **Sum of Adult + Pediatric.** Confirmed admissions only.
**Earliest Dates:**
• `_1d` (Daily): **2019-12-31**
• `_7dav` (7-Day Avg): **2020-01-06** |
+| **Suspected + Confirmed** | `sum_confirmed_suspected_admissions_covid` | **Sum of Adult + Pediatric.** Combined count of confirmed and suspected cases.
**Earliest Dates:**
• `_1d` (Daily): **2019-12-31**
• `_7dav` (7-Day Avg): **2020-01-06** |
+| **Influenza** | `confirmed_admissions_influenza` | All confirmed influenza hospital admissions.
**Earliest Dates:**
• `_1d` (Daily): **2020-01-02**
• `_7dav` (7-Day Avg): **2020-01-08** |
+
-*for all the above signals & 7-day average signals, their geography is state, and resolution is 1 day.
+> **Note**
+> * For all the above signals & 7-day average signals, their geography is state, and resolution is 1 day.
+> * The 7-day average signals are computed by Delphi by calculating moving averages of the preceding 7 days, so e.g. the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive.
+{: .note }
-The 7-day average signals are computed by Delphi by calculating
-moving averages of the preceding 7 days, so e.g. the signal for June 7 is the
-average of the underlying data for June 1 through 7, inclusive.
## Table of contents
{: .no_toc .text-delta}
diff --git a/docs/api/covidcast-signals/hospital-admissions.md b/docs/api/covidcast-signals/hospital-admissions.md
index 1dcd5959f..d35870e7d 100644
--- a/docs/api/covidcast-signals/hospital-admissions.md
+++ b/docs/api/covidcast-signals/hospital-admissions.md
@@ -8,15 +8,31 @@ nav_order: 1
# Hospital Admissions
{: .no_toc}
-* **Source name:** `hospital-admissions`
-* **Earliest issue available:** June 21, 2020
-* **Number of data revisions since May 19, 2020:** 1
-* **Date of last change:** October 20, 2020
-* **Available for:** county, hrr, msa, state (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)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `hospital-admissions` |
+| **Data Source** | Health system partners |
+| **Geographic Levels** | National, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Daily |
+| **Date of last data revision:** | October 20, 2020 (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-02-01 |
+| **License** | [CC BY](../covidcast_licensing.md#creative-commons-attribution) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+### October 20, 2020
+We went from a custom geo mapping file (for aggregating from zip->(county, msa, hrr, state)) to a central geo file based on rigorously sourced US census data.
+
+
## Overview
+{: .no_toc}
This data source is based on electronic medical records and claims data about
hospital admissions, provided to us by health system partners. We use this
@@ -26,12 +42,19 @@ COVID-associated diagnosis code in a given location, on a given day.
See also our [Health & Human Services](hhs.md) data source for official COVID
hospitalization reporting from the Department of Health & Human Services.
+**Active Signals.** These signals are currently updated.
+
| Signal | Description |
| --- | --- |
| `smoothed_covid19_from_claims` | Estimated percentage of new hospital admissions with COVID-associated diagnoses, based on claims data from health system partners, smoothed in time using a Gaussian linear smoother
**Earliest date available:** 2020-02-01 |
| `smoothed_adj_covid19_from_claims` | Same as `smoothed_covid19_from_claims`, but with systematic day-of-week effects removed using [the same mechanism as in `doctor-visits`](doctor-visits.md#day-of-week-adjustment)
**Earliest date available:** 2020-02-01 |
-| `smoothed_covid19` | Estimated percentage of new hospital admissions with COVID-associated diagnoses, based on electronic medical record and claims data from health system partners, smoothed in time using a Gaussian linear smoother. _This signal is no longer updated as of 1 October, 2020._
**Earliest date available:** 2020-02-01 |
-| `smoothed_adj_covid19` | Same as `smoothed_covid19`, but with systematic day-of-week effects removed using [the same mechanism as in `doctor-visits`](doctor-visits.md#day-of-week-adjustment). _This signal is no longer updated as of 1 October, 2020._
**Earliest date available:** 2020-02-01 |
+
+**Deprecated Signals.** These signals are frozen and no longer updated as of Oct 1, 2020.
+
+| Signal | Description |
+| --- | --- |
+| `smoothed_covid19` | Estimated percentage of new hospital admissions with COVID-associated diagnoses, based on electronic medical record and claims data from health system partners, smoothed in time using a Gaussian linear smoother.
**Earliest date available:** 2020-02-01 |
+| `smoothed_adj_covid19` | Same as `smoothed_covid19`, but with systematic day-of-week effects removed using [the same mechanism as in `doctor-visits`](doctor-visits.md#day-of-week-adjustment).
**Earliest date available:** 2020-02-01 |
## Table of Contents
{: .no_toc .text-delta}
diff --git a/docs/api/covidcast-signals/inactive.md b/docs/api/covidcast-signals/inactive.md
new file mode 100644
index 000000000..bebbb83ff
--- /dev/null
+++ b/docs/api/covidcast-signals/inactive.md
@@ -0,0 +1,12 @@
+---
+title: Inactive Sources (COVIDcast)
+parent: Data Sources and Signals
+grand_parent: Main Endpoint (COVIDcast)
+nav_order: 99
+has_children: true
+---
+
+# Inactive COVIDcast Sources
+{: .no_toc}
+
+These COVIDcast data sources and signals are no longer actively updated.
diff --git a/docs/api/covidcast-signals/indicator-combination.md b/docs/api/covidcast-signals/indicator-combination.md
index fe2edd3cf..dfc57f8ff 100644
--- a/docs/api/covidcast-signals/indicator-combination.md
+++ b/docs/api/covidcast-signals/indicator-combination.md
@@ -1,14 +1,21 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive Indicator Combination
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# Indicator Combination
{: .no_toc}
-* **Source name:** `indicator-combination`
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `indicator-combination` |
+| **Data Source** | Delphi |
+| **Geographic Levels** | State, County, Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - no longer updated since 2021-03-16 |
+| **Temporal Scope Start** | 2020-04-06 |
+| **License** | [CC BY](../covidcast_licensing.md#creative-commons-attribution) |
This source provides signals which are combinations of the other sources,
calculated or composed by Delphi. It is not a primary data source.
@@ -21,12 +28,27 @@ calculated or composed by Delphi. It is not a primary data source.
## Statistical Combination Signals
-* **Earliest issue available:** May 20, 2020
-* **Number of data revisions since May 19, 2020:** 1
-* **Date of last change:** [June 3, 2020](../covidcast_changelog.md#indicator-combination)
-* **Available for:** county, msa, state (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)
+| Attribute | Details |
+| :--- | :--- |
+| **Geographic Levels** | State, County, Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Date of last data revision:** | June 3, 2020 (see [data revision docs](#changelog)) |
+
+
+### Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+#### June 3, 2020
+
+Standard error is now included in the `nmf_day_doc_fbc_fbs_ght` signal for all geo levels and dates, representing the estimated uncertainty in this signal. This uncertainty comes about because the signal is a combination of other signals based on survey estimates or other estimates with margins of error.
+
+
+
+### Overview
+{: .no_toc}
These signals combine Delphi's indicators---*not* including cases and deaths,
but including other signals expected to be related to the underlying rate of
@@ -43,6 +65,7 @@ These signals were updated daily until March 17, 2021.
| `nmf_day_doc_fbc_fbs_ght` | This signal uses a rank-1 approximation, from a nonnegative matrix factorization approach, to identify an underlying signal that best reconstructs the Doctor Visits (`smoothed_adj_cli`), Facebook Symptoms surveys (`smoothed_cli`), Facebook Symptoms in Community surveys (`smoothed_hh_cmnty_cli`), and Search Trends (`smoothed_search`) indicators. It does not include official reports (cases and deaths from the `jhu-csse` source). Higher values of the combined signal correspond to higher values of the other indicators, but the scale (units) of the combination is arbitrary. Note that the Search Trends source is not available at the county level, so county values of this signal do not use it. This signal is deprecated and is no longer updated as of March 17, 2021.
**Earliest date available:** 2020-04-15 |
| `nmf_day_doc_fbs_ght` | This signal is calculated in the same way as `nmf_day_doc_fbc_fbs_ght`, but does *not* include the Symptoms in Community survey signal, which was not available at the time this signal was introduced. It also uses `smoothed_cli` from the `doctor-visits` source instead of `smoothed_adj_cli`. This signal is deprecated and is no longer updated as of May 27, 2020.
**Earliest date available:** 2020-04-06 |
+
### Estimation
Let $$x_{rs}(t)$$ denote the value of sensor $$s$$ on day $$t$$ in region $$r$$
@@ -191,11 +214,27 @@ The resampling method for each input source is as follows:
## Compositional Signals: Confirmed Cases and Deaths
-* **Earliest issue available:** 7 July 2020
-* **Number of data revisions since 19 May 2020:** 1
-* **Date of last change:** [12 October 2020](../covidcast_changelog.md#indicator-combination)
-* **Available for:** county, msa, hrr, state (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `indicator-combination` |
+| **Geographic Levels** | State, County, Metropolitan Statistical Area (MSA), U.S. HHS Region (see [geography coding docs](../covidcast_geography.md)) |
+| **Date of last data revision:** October 12, 2020 (see [data revision docs](#changelog-deaths)) |
+
+## Changelog Deaths
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+### October 12, 2020
+
+The 10 October 2020 issue of all `indicator-combination` deaths signals has been removed from the API. These signals are primarily constructed of USAFacts data, whose 10 October 2020 issue was discovered to be corrupt on 11 October and repaired on 12 October. Subsequent issues have adequate coverage of all regions and dates included in the 10 October issue, so this change only affects forecasters who intend to pull training data with an `as_of` or `issues` parameter set to 20201010.
+
+
+
+
+## Overview
These signals combine the cases and deaths data from JHU and USA Facts. This is
a straight composition: the signals below use the [JHU signal data](jhu-csse.md)
diff --git a/docs/api/covidcast-signals/jhu-csse.md b/docs/api/covidcast-signals/jhu-csse.md
index c9d665b5a..c4d572f98 100644
--- a/docs/api/covidcast-signals/jhu-csse.md
+++ b/docs/api/covidcast-signals/jhu-csse.md
@@ -1,20 +1,49 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive JHU Cases and Deaths
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# JHU Cases and Deaths
{: .no_toc}
-* **Source name:** `jhu-csse`
-* **Earliest issue available:** May 7, 2020
-* **Number of data revisions since May 19, 2020:** 1
-* **Date of last change:** [October 7, 2020](../covidcast_changelog.md#jhu-csse)
-* **Available for:** county, hrr, msa, state, hhs, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** [CC BY](#source-and-licensing)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `jhu-csse` |
+| **Data Source** | JHU CSSE |
+| **Geographic Levels** | National, U.S. HHS Region, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2023-03-09 |
+| **Date of last data revision:** | October 7, 2020 (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-01-22, with some variation by geographic area |
+| **License** | [CC BY](#source-and-licensing) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+### October 7, 2020
+
+The following changes were made to all `jhu-csse` signals related to geocoding:
+- NY Boroughs county FIPS (36005, 36047, 36061, 36081, 36085) are now [differentiated by JHU](https://github.com/CSSEGISandData/COVID-19/issues/3084),
+- “Unassigned” and “Out of State” counts are assigned to a megaFIPS at the county level (XX000 where XX is the state FIPS code) and will now be incorporated into the state totals
+- The split of the Kansas City, Missouri into its four sub-counties is now done with a more precise population proportion,
+- The split of the Dukes and Nantucket, Massachusetts FIPS codes into the two sub-counties is now done with a more precise population proportion,
+- Some counts are reported in the Utah territories JHU UIDs 84070015-84070020. These are now aggregated properly into the state megaFIPS 49000, which will be aggregated in state-level information.
+
+### September 1, 2020
+
+NY Boroughs county FIPS (36005, 36047, 36061, 36081, 36085) are now split in proportion to the population of each county, instead of being reported in aggregate in FIPS 36061.
+
+### June 3, 2020
+
+We now include figures on Puerto Rico for all `jhu-csse` signals at the state level.
+
+
+
## Overview
diff --git a/docs/api/covidcast-signals/nchs-mortality.md b/docs/api/covidcast-signals/nchs-mortality.md
index 94a72ead2..5b910cacb 100644
--- a/docs/api/covidcast-signals/nchs-mortality.md
+++ b/docs/api/covidcast-signals/nchs-mortality.md
@@ -8,13 +8,29 @@ nav_order: 1
# NCHS Mortality Data
{: .no_toc}
-* **Source name:** `nchs-mortality`
-* **Earliest issue available:** Epiweek 50 2020 (6-12 December 2020)
-* **Number of data revisions since May 19, 2020:** 0
-* **Date of last change:** Never
-* **Available for:** state (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** week (see [date format docs](../covidcast_times.md))
-* **License:** [NCHS Data Use Agreement](https://www.cdc.gov/nchs/data_access/restrictions.htm)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `nchs-mortality` |
+| **Data Source** | [National Center for Health Statistics (NCHS)](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm) |
+| **Geographic Levels** | State (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Weekly (see [date format docs](../covidcast_times.md))|
+| **Reporting Cadence** | Weekly |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020w05 with some variation by geography |
+| **License** | [NCHS Data Use Agreement](https://www.cdc.gov/nchs/data_access/restrictions.htm) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
+
+## Overview
This data source of national provisional death counts is based on death
certificate data received and coded by the National Center for Health Statistics
@@ -71,7 +87,7 @@ We report the NCHS Mortality data in a weekly format (`time_type=week` &
`time_value={YYYYWW}`, where `YYYYWW` refers to an epiweek). The CDC defines
the [epiweek](https://web.archive.org/web/20210623224758/https://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf) as
seven days, from Sunday to Saturday. We check the week-ending dates provided in
-the NCHS morality data and use Python package
+the NCHS mortality data and use Python package
[epiweeks](https://pypi.org/project/epiweeks/) to convert them into epiweek
format.
diff --git a/docs/api/covidcast-signals/nhsn.md b/docs/api/covidcast-signals/nhsn.md
index 2fc89afd7..313efa282 100644
--- a/docs/api/covidcast-signals/nhsn.md
+++ b/docs/api/covidcast-signals/nhsn.md
@@ -7,15 +7,31 @@ nav_order: 1
# National Healthcare Safety Network Respiratory Hospitalizations
{: .no_toc}
-* **Source name:** `nhsn`
-* **Earliest issue available:** November 19, 2024
-* **Number of data revisions since 18 Nov 2024:** 0
-* **Date of last change:** Never
-* **Available for:** state, hhs, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** week (see [date format docs](../covidcast_times.md))
-* **License:** [Public Domain US Government](https://www.usa.gov/government-works)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `nhsn` |
+| **Data Source** | [The National Healthcare Safety Network (NHSN)](https://www.cdc.gov/nhsn/index.html) |
+| **Geographic Levels** | National, U.S. HHS Region, State (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Weekly (Sunday to Saturday) (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Weekly |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-08-08 |
+| **License** | [Public Domain US Government](https://www.usa.gov/government-works) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
+
## Overview
+{: .no_toc}
[The National Healthcare Safety Network (NHSN)](https://www.cdc.gov/nhsn/index.html) is the nation’s most widely used healthcare-associated infection tracking system.
This dataset reports preliminary and finalized weekly hospital respiratory data and metrics aggregated to national and state/territory levels reported to the CDC’s National Health Safety Network (NHSN). Values are available for reference dates beginning August 2020.
@@ -30,21 +46,27 @@ 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.
+### Available Signals
+{: .no_toc}
-| 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 |
-| `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.
**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.
**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.
**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.
**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.
**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.
**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.
**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.
**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.
**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.
**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.
**Earliest date available:** 2020-08-08 |
+* **Reporting Cutoffs:**
+ * **Finalized Signals:** Data received by Friday/Saturday of the following week (~6-7 day lag).
+ * **Preliminary (`_prelim`) Signals:** Data received by Wednesday of the following week (~4 day lag).
+
+| Signal Name | Pathogen | Metric Description | Version |
+| :--- | :--- | :--- | :--- |
+| `confirmed_admissions_covid_ew` | COVID-19 | **Patient Count:** Total hospitalized patients. | Finalized |
+| `confirmed_admissions_covid_ew_prelim` | COVID-19 | **Patient Count:** Total hospitalized patients. | Preliminary |
+| `hosprep_confirmed_admissions_covid_ew` | COVID-19 | **Facility Count:** Number of hospitals reporting admissions. | Finalized |
+| `hosprep_confirmed_admissions_covid_ew_prelim` | COVID-19 | **Facility Count:** Number of hospitals reporting admissions. | Preliminary |
+| `confirmed_admissions_flu_ew` | Influenza | **Patient Count:** Total hospitalized patients. | Finalized |
+| `confirmed_admissions_flu_ew_prelim` | Influenza | **Patient Count:** Total hospitalized patients. | Preliminary |
+| `hosprep_confirmed_admissions_flu_ew` | Influenza | **Facility Count:** Number of hospitals reporting admissions. | Finalized |
+| `hosprep_confirmed_admissions_flu_ew_prelim` | Influenza | **Facility Count:** Number of hospitals reporting admissions. | Preliminary |
+| `confirmed_admissions_rsv_ew` | RSV | **Patient Count:** Total hospitalized patients. | Finalized |
+| `confirmed_admissions_rsv_ew_prelim` | RSV | **Patient Count:** Total hospitalized patients. | Preliminary |
+| `hosprep_confirmed_admissions_rsv_ew` | RSV | **Facility Count:** Number of hospitals reporting admissions. | Finalized |
+| `hosprep_confirmed_admissions_rsv_ew_prelim` | RSV | **Facility Count:** Number of hospitals reporting admissions. | Preliminary |
## Table of Contents
diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md
index 8e988a25b..99d2056b1 100644
--- a/docs/api/covidcast-signals/nssp.md
+++ b/docs/api/covidcast-signals/nssp.md
@@ -7,31 +7,49 @@ nav_order: 1
# National Syndromic Surveillance Program Emergency Department Visits
{: .no_toc}
-* **Source name:** `nssp`
-* **Earliest issue available:** April 17, 2024
-* **Number of data revisions since 19 May 2020:** 0
-* **Date of last change:** Never
-* **Available for:** county, hrr, msa, state, hhs, nation (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** week (see [date format docs](../covidcast_times.md))
-* **License:** [Public Domain US Government](https://www.usa.gov/government-works)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `nssp` |
+| **Data Source** | [The National Syndromic Surveillance Program (NSSP)](https://www.cdc.gov/nssp/php/about/index.html) |
+| **Geographic Levels** | National, U.S. HHS Region, State (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Weekly (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Weekly |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2022-10-01 |
+| **License** | [Public Domain US Government](https://www.usa.gov/government-works) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes so far.
+
+
## Overview
+{: .no_toc}
[The National Syndromic Surveillance Program (NSSP)](https://www.cdc.gov/nssp/php/about/index.html) is an effort to track epidemiologically relevant conditions.
This dataset in particular tracks emergency department (ED) visits arising from a subset of influenza-like illnesses, specifically influenza, COVID-19, and respiratory syncytial virus (RSV).
It is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data), which started reporting data in late 2022.
As of May 2024, NSSP received data from 78% of US EDs.
-| Signal | Description |
-|---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------|
-| `pct_ed_visits_covid` | Percent of ED visits that had a discharge diagnosis code of COVID-19
**Earliest date available:** 2022-10-01 |
-| `pct_ed_visits_influenza` | Percent of ED visits that had a discharge diagnosis code of influenza
**Earliest date available:** 2022-10-01 |
-| `pct_ed_visits_rsv` | Percent of ED visits that had a discharge diagnosis code of rsv
**Earliest date available:** 2022-10-01 |
-| `pct_ed_visits_combined` | Percent of ED visits that had a discharge diagnosis code of COVID-19, influenza, or rsv
**Earliest date available:** 2022-10-01 |
-| `smoothed_pct_ed_visits_covid` | 3 week moving average of `pct_ed_visits_covid`
**Earliest date available:** 2022-10-01 |
-| `smoothed_pct_ed_visits_influenza` | 3 week moving average of `pct_ed_visits_influenza`
**Earliest date available:** 2022-10-01 |
-| `smoothed_pct_ed_visits_rsv` | 3 week moving average of `pct_ed_visits_rsv`
**Earliest date available:** 2022-10-01 |
-| `smoothed_pct_ed_visits_combined` | 3 week moving average of `pct_ed_visits_combined`
**Earliest date available:** 2022-10-01 |
+
+### Available Signals
+{: .no_toc}
+
+* **Raw Signals** (`pct_ed_visits_...`) represent the weekly percentage of ED visits for the specific pathogen.
+* **Smoothed Signals** (`smoothed_pct_ed_visits_...`) represent a **3-week moving average** of the raw signal.
+
+| Signal Pair (Raw / Smoothed) | Pathogen | Description |
+| :--- | :--- | :--- |
+| `pct_ed_visits_covid`
`smoothed_pct_ed_visits_covid` | **COVID-19** | Percentage of ED visits with a discharge diagnosis of COVID-19. |
+| `pct_ed_visits_influenza`
`smoothed_pct_ed_visits_influenza` | **Influenza** | Percentage of ED visits with a discharge diagnosis of Influenza. |
+| `pct_ed_visits_rsv`
`smoothed_pct_ed_visits_rsv` | **RSV** | Percentage of ED visits with a discharge diagnosis of RSV. |
+| `pct_ed_visits_combined`
`smoothed_pct_ed_visits_combined` | **Combined** | Percentage of ED visits with a diagnosis of **any** of the above (COVID, Flu, or RSV). | |
## Table of Contents
{: .no_toc .text-delta}
diff --git a/docs/api/covidcast-signals/quidel.md b/docs/api/covidcast-signals/quidel.md
index 430339291..3894ae71e 100644
--- a/docs/api/covidcast-signals/quidel.md
+++ b/docs/api/covidcast-signals/quidel.md
@@ -8,25 +8,45 @@ nav_order: 1
# Quidel
{: .no_toc}
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `quidel` |
+| **Data Source** | QuidelOrtho Corp. |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **License** | [CC BY](../covidcast_licensing.md#creative-commons-attribution) |
+
## Table of Contents
{: .no_toc .text-delta}
1. TOC
{:toc}
-## Accessibility: Delphi-internal only
+**Accessibility: Delphi-internal only**
## Quidel COVID-19 Tests
+{: .no_toc}
+
+| Attribute | Details |
+| :--- | :--- |
+| **Geographic Levels** | National, U.S. HHS Region, State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Reporting Cadence** | Daily |
+| **Date of last data revision:** | October 22, 2020 (see [data revision docs](#changelog-covid-19-tests)) |
+| **Temporal Scope Start** | 2020-05-26 |
+
+### Changelog COVID-19 Tests
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+#### October 22, 2020
+We went from a custom geo mapping file (for aggregating from zip->(county, msa, hrr, state)) to a central geo file based on rigorously sourced US census data.
-* **Source name:** `quidel`
-* **Earliest issue available:** July 29, 2020
-* **Number of data revisions since May 19, 2020:** 1
-* **Date of last change:** October 22, 2020
-* **Available for:** county, hrr, msa, state, HHS, 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)
+
### Overview
+{: .no_toc}
Data source based on COVID-19 Antigen tests, provided to us by Quidel, Inc. When
a patient (whether at a doctor’s office, clinic, or hospital) has COVID-like
@@ -54,7 +74,7 @@ meaningful levels starting May 26, 2020.
| `covid_ag_smoothed_pct_positive_age_65plus` | Percentage of antigen tests that were positive for COVID-19 (ages 65+), smoothed by pooling together the last 7 days of tests.
**Earliest date available:** 2020-05-26 |
| `covid_ag_smoothed_pct_positive_age_0_17` | Percentage of antigen tests that were positive for COVID-19 (ages 0-17), smoothed by pooling together the last 7 days of tests.
**Earliest date available:** 2020-05-26 |
-### Estimation
+## Estimation
The source data from which we derive our estimates contains a number of features
for every test, including localization at 5-digit Zip Code level, a TestDate and
@@ -80,7 +100,7 @@ We estimate p across 6 temporal-spatial aggregation schemes:
- daily, at the HHS level;
- daily, at the US national level.
-#### Standard Error
+### Standard Error
We assume the estimates for each time point follow a binomial distribution. The
estimated standard error then is:
@@ -89,11 +109,11 @@ $$
\text{se} = 100 \sqrt{ \frac{\frac{p}{100}(1- \frac{p}{100})}{N} }
$$
-#### Smoothing
+### Smoothing
We add two kinds of smoothing to the smoothed signals:
-##### Temporal Smoothing
+#### Temporal Smoothing
Smoothed estimates are formed by pooling data over time. That is, daily, for
each location, we first pool all data available in that location over the last 7
days, and we then recompute everything described in the two subsections above.
@@ -101,7 +121,7 @@ days, and we then recompute everything described in the two subsections above.
Pooling in this way makes estimates available in more geographic areas, as many areas
report very few tests per day, but have enough data to report when 7 days are considered.
-##### Geographical Smoothing
+#### Geographical Smoothing
**County, MSA and HRR levels**: In a given County, MSA or HRR, suppose $$N$$ COVID tests
are taken in a certain time period, $$X$$ is the number of tests taken with positive
@@ -165,15 +185,25 @@ that day will not include it.
These signals are inactive. They were updated until May 19, 2020.
-* **Source name:** `quidel`
-* **Earliest issue available:** April 29, 2020
-* **Last issued:** May 19, 2020
-* **Number of data revisions since May 19, 2020:** 0
-* **Date of last change:** Never
-* **Available for:** msa, state (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
+| Attribute | Details |
+| :--- | :--- |
+| **Geographic Levels** | State, Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2020-05-01 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog-flu-tests)) |
+| **Temporal Scope Start** | 2020-01-31 |
+
+### Changelog Flu Tests
+
+
+Click to expand
+
+#### October 22, 2020
+We went from a custom geo mapping file (for aggregating from zip->(county, msa, hrr, state)) to a central geo file based on rigorously sourced US census data.
+
+
### Overview
+{: .no_toc}
Data source based on flu lab tests, provided to us by Quidel, Inc. When a
patient (whether at a doctor’s office, clinic, or hospital) has COVID-like
diff --git a/docs/api/covidcast-signals/safegraph.md b/docs/api/covidcast-signals/safegraph.md
index 96775de0f..f8369f91a 100644
--- a/docs/api/covidcast-signals/safegraph.md
+++ b/docs/api/covidcast-signals/safegraph.md
@@ -1,16 +1,20 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive SafeGraph
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# SafeGraph
{: .no_toc}
-* **Source name:** `safegraph`
-* **Available for:** county, MSA, HRR, state (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)
+
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `safegraph` |
+| **Data Source** | SafeGraph |
+| **Geographic Levels** | State, County, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md))|
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Temporal Scope Start** | January 1st, 2019 |
+| **License** | [CC BY](../covidcast_licensing.md#creative-commons-attribution) |
This data source uses data reported by [SafeGraph](https://www.safegraph.com/)
using anonymized location data from mobile phones. From June 2020-July 2022,
@@ -25,11 +29,29 @@ surface signals from two such datasets.
## SafeGraph Social Distancing Metrics
-* **Earliest issue available:** June 20, 2020
-* **Number of data revisions since June 23, 2020:** 1
-* **Date of last change:** November 3, 2020
+| Attribute | Details |
+| **Date of last data revision:** | November 3rd, 2020 (see [data revision docs](#changelog-social-distancing-metrics)) |
+| **Reporting Cadence** | Inactive - No longer updated after April 19th, 2021. |
+
+### Changelog (Social Distancing Metrics)
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+#### April 19th, 2021
+
+The Safegraph social distancing metrics are no longer being updated. Weekly patterns are still available.
+
+#### November 3rd, 2020
+
+We went from a custom geo mapping file (for aggregating from county->state) to a central geo file based on rigorously sourced US census data.
+
+
-**This dataset is no longer updated after April 19th, 2021.**
+### Overview
+{: .no_toc}
Data source based on the [Social Distancing Metrics](https://docs.safegraph.com/docs/social-distancing-metrics) data product. SafeGraph
provided this data for individual census block groups, using differential
@@ -76,11 +98,28 @@ additional day for SafeGraph's data to be ingested into the COVIDcast API.
## SafeGraph Weekly Patterns
-* **Earliest issue available:** November 30, 2020
-* **Number of data revisions since June 23, 2020:** 0
-* **Date of last change:** never
+| Attribute | Details |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog-weekly-patterns)) |
+| **Reporting Cadence** | Inactive - No longer updated after May 5th, 2022 |
+
+### Changelog (Weekly Patterns)
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+#### July 15th, 2022
+The Safegraph Weekly Patterns dataset is no longer updated.
-**This dataset is no longer updated after July 15th, 2022.**
+#### November 3rd, 2020
+
+We went from a custom geo mapping file (for aggregating from county->state) to a central geo file based on rigorously sourced US census data.
+
+
+
+### Overview
+{: .no_toc}
Data source based on [Weekly
Patterns](https://docs.safegraph.com/docs/weekly-patterns) dataset. SafeGraph
diff --git a/docs/api/covidcast-signals/usa-facts.md b/docs/api/covidcast-signals/usa-facts.md
index 3c972cfcd..f7763c93f 100644
--- a/docs/api/covidcast-signals/usa-facts.md
+++ b/docs/api/covidcast-signals/usa-facts.md
@@ -1,20 +1,41 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive USAFacts Cases and Deaths
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
# USAFacts Cases and Deaths
{: .no_toc}
-* **Source name:** `usa-facts`
-* **Earliest issue available:** June 24, 2020
-* **Number of data revisions since May 19, 2020:** 2
-* **Date of last change:** [November 3, 2020](../covidcast_changelog.md#usa-facts)
-* **Available for:** county, hrr, msa, state (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** [CC BY](#source-and-licensing)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `usa-facts` |
+| **Data Source** | [USAFacts](https://usafacts.org/) |
+| **Geographic Levels** | National, U.S. HHS Region, State/ADM 1, County/ADM 2, Hospital Referral Region (HRR), Metropolitan Statistical Area (MSA) (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated since 2023-01-02 |
+| **Date of last data revision:** | November 3, 2020 (see [data revision docs](#changelog)) |
+| **Temporal Scope Start** | 2020-01-25 |
+| **License** | [CC BY](#source-and-licensing) |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+### November 3, 2020
+We went from a custom geo mapping file (for aggregating from county->(msa, hrr, state)) to a central geo file based on rigorously sourced US census data.
+
+### October 12, 2020
+
+The 10 October 2020 issue of all `usa-facts` deaths signals has been removed from the API. The file for deaths provided by USAFacts on 10 October included case data instead. The resulting spurious 100× increase in magnitude of COVIDcast `usa-facts` deaths signals was noticed on 11 October and repaired on 12 October. Subsequent issues have adequate coverage of all regions and dates included in the 10 October issue, so this change only affects forecasters that intend to pull training data with an `as_of` or `issues` parameter set to 20201010.
+
+
+
+
+## Overview
This data source of confirmed COVID-19 cases and deaths is based on reports made
available by [USAFacts](https://usafacts.org/).
diff --git a/docs/api/covidcast-signals/youtube-survey.md b/docs/api/covidcast-signals/youtube-survey.md
index 5b376f913..27c86fd63 100644
--- a/docs/api/covidcast-signals/youtube-survey.md
+++ b/docs/api/covidcast-signals/youtube-survey.md
@@ -1,8 +1,7 @@
---
+parent: Inactive Sources (COVIDcast)
+grand_parent: Data Sources and Signals
title: inactive Youtube Survey
-parent: Data Sources and Signals
-grand_parent: Main Endpoint (COVIDcast)
-nav_order: 2
---
[//]: # (code at https://github.com/cmu-delphi/covid-19/tree/deeb4dc1e9a30622b415361ef6b99198e77d2a94/youtube)
@@ -10,13 +9,27 @@ nav_order: 2
# Youtube Survey
{: .no_toc}
-* **Source name:** `youtube-survey`
-* **Earliest issue available:** May 01, 2020
-* **Number of data revisions since May 19, 2020:** 0
-* **Date of last change:** Never
-* **Available for:** state (see [geography coding docs](../covidcast_geography.md))
-* **Time type:** day (see [date format docs](../covidcast_times.md))
-* **License:** [CC BY-NC](../covidcast_licensing.md#creative-commons-attribution-noncommercial)
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `youtube-survey` |
+| **Data Source** | Google/Delphi |
+| **Geographic Levels** | State (see [geography coding docs](../covidcast_geography.md)) |
+| **Temporal Granularity** | Daily (see [date format docs](../covidcast_times.md)) |
+| **Reporting Cadence** | Inactive - No longer updated after June 22nd, 2020 |
+| **Date of last data revision:** | Never (see [data revision docs](#changelog)) |
+| **License** | [CC BY-NC](../covidcast_licensing.md#creative-commons-attribution-noncommercial) |
+| **Temporal Scope Start** | April 21st, 2020 |
+
+## Changelog
+
+
+Click to expand
+
+See [COVIDcast Signal Changes](../covidcast_changelog.md) for general information about how we track changes to signals.
+
+No changes have been made to this signal.
+
+
## Overview
diff --git a/docs/api/covidcast.md b/docs/api/covidcast.md
index d283fb8a8..8415adfb8 100644
--- a/docs/api/covidcast.md
+++ b/docs/api/covidcast.md
@@ -1,7 +1,7 @@
---
title: Main Endpoint (COVIDcast)
has_children: true
-nav_order: 2
+nav_order: 1
---
# Main Epidata API
@@ -18,15 +18,8 @@ selected geographical areas---counties, states, metropolitan statistical areas,
and other divisions.
-Get
-updates: Delphi operates a
mailing
-list for users of the COVIDcast API. We will use the list to announce API
-changes, corrections to data, and new features; API users may also use the
-mailing list to ask general questions about its use. If you use the API, we
-strongly encourage you to
subscribe.
-
+> **Get updates:** Delphi operates a [mailing list](https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api) for users of the COVIDcast API. We will use the list to announce API changes, corrections to data, and new features; API users may also use the mailing list to ask general questions about its use. If you use the API, we strongly encourage you to [subscribe](https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api).
+{: .important }
## Table of contents
{: .no_toc .text-delta}
@@ -53,16 +46,15 @@ CSV file.
Several [API clients are available](covidcast_clients.md) for common programming
languages, so you do not need to construct API calls yourself to obtain
COVIDcast data. Once you install the appropriate client for your programming
-language, accessing data is as easy as, in [R](https://www.r-project.org/):
-
-```r
-library(epidatr)
+language, accessing data is as easy as:
-data <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
- time_values = c(20200401, 20200405:20200414))
-```
+
+
-or, in [Python](https://www.python.org):
+
```python
from epidatpy import EpiDataContext, EpiRange
@@ -78,12 +70,23 @@ apicall = epidata.pub_covidcast(
)
data = apicall.df()
```
+
+
+
+
+```r
+library(epidatr)
+
+data <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
+ time_values = c(20200401, 20200405:20200414))
+```
+
+
+
-Python users seeking to use the COVIDcast API to fetch data should instead
-consider using the [dedicated API client](covidcast_clients.md), which provides
-a `metadata()` method to return metadata as a data frame.
+
Optionally install the package using pip(env):
````bash
@@ -110,12 +102,9 @@ from delphi_epidata import Epidata
res = Epidata.covidcast_meta()
print(res['result'], res['message'], len(res['epidata']))
````
+
-### R
-
-R users seeking to use the COVIDcast API to fetch data should instead consider
-using the [dedicated API client](covidcast_clients.md), which provides a
-`covidcast_meta()` function to return metadata as a data frame.
+
````R
# Import
@@ -124,3 +113,20 @@ source('delphi_epidata.R')
res <- Epidata$covidcast_meta()
cat(paste(res$result, res$message, length(res$epidata), "\n"))
````
+
+
+
+
+````html
+
+
+
+
+````
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.delphi('ec', 201501)
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_delphi(system = 'ec', epiweek = 201501)
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+Place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.delphi('ec', 201501)
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$delphi(system = 'ec', epiweek = 201501)
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
*Note: Data availability varies by country.* |
+| **Temporal Granularity** | Weekly (Epiweek) |
+| **Reporting Cadence** | Inactive - No longer updated since 2020w32|
+| **Temporal Scope Start** | 2014w04 |
+| **License** | [CC BY](https://creativecommons.org/licenses/by/4.0/) |
+
+
+## Overview
+{: .no_toc}
+
+This endpoint provides digital surveillance sensor estimates for dengue activity, derived from various data streams.
General topics not specific to any particular endpoint are discussed in the
[API overview](README.md). Such topics include:
[contributing](README.md#contributing), [citing](README.md#citing), and
[data licensing](README.md#data-licensing).
-## Delphi's Dengue Digital Surveillance Sensors Data
+### Available Signals
-...
+The following signals are available:
+
+| Name | Description |
+| :--- | :--- |
+| `gft` | Google Flu Trends |
+| `ght` | Google Health Trends |
+| `twtr` | HealthTweets |
+| `wiki` | Wikipedia access |
+| `cdc` | CDC Page Hits |
+| `epic` | Epicast 1-week-ahead point prediction |
+| `quid` | Flu lab test data |
+| `sar3` | Seasonal Autoregression (order 3) |
+| `arch` | Best-fit Archetype at 1-week-ahead |
+
+## Table of contents
+{: .no_toc .text-delta}
+
+1. TOC
+{:toc}
# The API
-The base URL is: https://api.delphi.cmu.edu/epidata/dengue_sensors/
+The base URL is:
-See [this documentation](README.md) for details on specifying epiweeks, dates, and lists.
## Parameters
### Required
-
+| Parameter | Description | Type |
+| --- | --- | --- |
+| `auth` | password | string |
+| `epiweeks` | epiweeks (see [Date Formats](date_formats.html)) | `list` of epiweeks |
+| `name` | name | `list` of names (see [Available Signals](#available-signals)) |
+| `locations` | locations | `list` of location labels (see [Geographic Codes](geographic_codes.html#countries-and-territories-in-the-americas)) |
+
## Response
-| Field | Description | Type |
-|-----------|-----------------------------------------------------------------|------------------|
-| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
-| `epidata` | list of results | array of objects |
-| ... | ... | ... |
-| `message` | `success` or error message | string |
+| Field | Description | Type |
+|-----------------------|-----------------------------------------------------------------|------------------|
+| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
+| `epidata` | list of results | array of objects |
+| `epidata[].location` | location label | string |
+| `epidata[].epiweek` | epiweek | integer |
+| `epidata[].name` | name | string |
+| `epidata[].value` | value | float |
+| `message` | `success` or error message | string |
# Example URLs
-
+### Dengue Sensors on 2015w01 (Puerto Rico)
+
+
+```json
+{
+ "result": 1,
+ "epidata": [
+ {
+ "location": "pr",
+ "epiweek": 201501,
+ "name": "ght",
+ "value": 103.676
+ }
+ ],
+ "message": "success"
+}
+```
# Code Samples
-
+Libraries are available for [R](https://cmu-delphi.github.io/epidatr/) and [Python](https://cmu-delphi.github.io/epidatpy/).
+The following samples show how to import the library and fetch Dengue Sensors data for Puerto Rico for epiweek `201501`.
+
+
+
+
+
+
+Install the package using pip:
+
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.dengue_sensors('auth_token', ['ght'], ['pr'], [201501])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_dengue_sensors(auth = 'auth_token', names = 'ght', locations = 'pr', epiweeks = 201501)
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.dengue_sensors('auth_token', ['gft'], ['pr'], [201501])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$dengue_sensors(auth = "auth_token", sensors = list("gft"), locations = list("pr"), epiweeks = list(201501))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
*Note: Data availability varies by country.* |
+| **Temporal Granularity** | Weekly (Epiweek) |
+| **Reporting Cadence** | Inactive - No longer updated since 2020w32 |
+| **Temporal Scope Start** | 2014w09 |
+| **License** | [CC BY](https://creativecommons.org/licenses/by/4.0/) |
+
+
+## Overview
+{: .no_toc}
+
+This endpoint provides nowcast esimtates of dengue incidence, based on historical data and reported case counts.
General topics not specific to any particular endpoint are discussed in the
[API overview](README.md). Such topics include:
[contributing](README.md#contributing), [citing](README.md#citing), and
[data licensing](README.md#data-licensing).
-## Delphi's Dengue Nowcast Data
+## Table of contents
+{: .no_toc .text-delta}
-...
+1. TOC
+{:toc}
# The API
-The base URL is: https://api.delphi.cmu.edu/epidata/dengue_nowcast/
+The base URL is:
-See [this documentation](README.md) for details on specifying epiweeks, dates, and lists.
## Parameters
### Required
-
+| Parameter | Description | Type |
+| --- | --- | --- |
+| `epiweeks` | epiweeks (see [Date Formats](date_formats.html)) | `list` of epiweeks |
+| `locations` | locations | `list` of location labels (see [Geographic Codes](geographic_codes.html#countries-and-territories-in-the-americas)) |
## Response
-| Field | Description | Type |
-|-----------|-----------------------------------------------------------------|------------------|
-| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
-| `epidata` | list of results | array of objects |
-| ... | ... | ... |
-| `message` | `success` or error message | string |
+| Field | Description | Type |
+|-----------------------|-----------------------------------------------------------------|------------------|
+| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
+| `epidata` | list of results | array of objects |
+| `epidata[].location` | location label | string |
+| `epidata[].epiweek` | epiweek | integer |
+| `epidata[].value` | nowcast value | float |
+| `epidata[].std` | standard deviation | float |
+| `message` | `success` or error message | string |
# Example URLs
-
+### Dengue Nowcast on 2015w01 (Puerto Rico)
+
+
+```json
+{
+ "result": 1,
+ "epidata": [
+ {
+ "location": "pr",
+ "epiweek": 201501,
+ "value": 12.34,
+ "std": 1.23
+ }
+ ],
+ "message": "success"
+}
+```
# Code Samples
-
+Libraries are available for [R](https://cmu-delphi.github.io/epidatr/) and [Python](https://cmu-delphi.github.io/epidatpy/).
+The following samples show how to import the library and fetch Dengue Nowcast data for Puerto Rico for epiweeks `201401` to `202301`.
+
+
+
+
+
+
+Install the package using pip:
+
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.dengue_nowcast(['pr'], EpiRange(201401, 202301))
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_dengue_nowcast(locations = 'pr', epiweeks = epirange(201401, 202301))
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.dengue_nowcast(['pr'], [201501])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$dengue_nowcast(locations = list("pr"), epiweeks = list(201501))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.sensors(['nat'], ['sar3'], EpiRange(201501, 202001))
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_sensors(auth = 'SECRET_API_AUTH_SENSORS', locations = 'nat',
+names = 'sar3', epiweeks = epirange(201501, 202001))
+print(res)
+```
+
-### Python
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.sensors(['nat'], ['sar3'], [201940, Epidata.range(202001, 202010)])
+res = Epidata.sensors(['nat'], ['sar3'], Epidata.range(201501, 202001))
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
-### R
+
-````R
-# Import
-source('delphi_epidata.R')
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$sensors(list('nat'), list('sar3') list(201940, Epidata$range(202001, 202010)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$sensors(locations = list("nat"), sensors = list("sar3"), epiweeks = Epidata$range(201501, 202001))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.ecdc_ili(['austria'], [202001, 202002])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_ecdc_ili(regions = 'austria', epiweeks = c(202001, 202002))
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.ecdc_ili(['austria'], [202001, 202002])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$ecdc_ili(regions = list("austria"), epiweeks = list(202001, 202002))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_flusurv(locations="CA", epiweeks=EpiRange(201701, 201801))
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_flusurv(locations = "CA", epiweeks = epirange(201701, 201801))
+print(res)
+```
+
-### JavaScript (in a web browser)
+
-````html
+The JavaScript client is available [here](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js).
+
+```html
-````
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.flusurv(['ca'], [201940, Epidata.range(202001, 202010)])
+res = Epidata.flusurv(['CA'], [Epidata.range(201701, 201801)])
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
-### R
+
-````R
-# Import
-source('delphi_epidata.R')
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$flusurv(list('ca'), list(201940, Epidata$range(202001, 202010)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$flusurv(locations = list("CA"), epiweeks = list(Epidata$range(201701, 201801)))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_fluview(regions="nat", epiweeks=EpiRange(201501, 201510))
+print(res)
+```
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_fluview(regions = "nat", epiweeks = epirange(201501, 201510))
+print(res)
+```
+
-### JavaScript (in a web browser)
+
-````html
+The JavaScript client is available [here](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js).
+
+```html
-````
+ EpidataAsync.fluview('nat', [EpidataAsync.range(201501, 201510)]).then((res) => {
+
+
+### Legacy Clients
-### Python
+We recommend using the modern client libraries mentioned above. Legacy clients are also available for [Python](https://pypi.org/project/delphi-epidata/), [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R), and [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.js).
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.fluview(['nat'], [201440, Epidata.range(201501, 201510)])
+res = Epidata.fluview(['nat'], [Epidata.range(201501, 201510)])
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
-### R
+
-````R
-# Import
-source('delphi_epidata.R')
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$fluview(list('nat'), list(201440, Epidata$range(201501, 201510)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$fluview(regions = list("nat"), epiweeks = list(Epidata$range(201501, 201510)))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
diff --git a/docs/api/fluview_clinical.md b/docs/api/fluview_clinical.md
index ca2b7b801..e42c23f98 100644
--- a/docs/api/fluview_clinical.md
+++ b/docs/api/fluview_clinical.md
@@ -2,29 +2,45 @@
title: FluView Clinical
parent: Data Sources and Signals
grand_parent: Other Endpoints (COVID-19 and Other Diseases)
-nav_order: 1
+nav_order: 2
---
# FluView Clinical
+{: .no_toc}
-This is the API documentation for accessing the FluView Clinical
-(`fluview_clinical`) endpoint of [Delphi](https://delphi.cmu.edu/)'s
-epidemiological data.
+
+| Attribute | Details |
+| :--- | :--- |
+| **Source Name** | `fluview_clinical` |
+| **Data Source** | [United States Centers for Disease Control and Prevention (CDC)](http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html) |
+| **Geographic Levels** | National, HHS regions, states, and Census divisions (see [Geographic Codes](geographic_codes.html#us-regions-and-states)) |
+| **Temporal Granularity** | Weekly (Epiweek) |
+| **Reporting Cadence** | Weekly (typically Fridays) |
+| **Temporal Scope Start** | 2016w40 |
+| **License** | [Publicly Accessible US Government](https://www.usa.gov/government-works) |
+
+
+## Overview
+{: .no_toc}
+
+This data source provides age-stratified clinical data on laboratory-confirmed influenza from the US Flu View system.
General topics not specific to any particular endpoint are discussed in the
[API overview](README.md). Such topics include:
[contributing](README.md#contributing), [citing](README.md#citing), and
[data licensing](README.md#data-licensing).
-## FluView Clinical Data
+## Table of contents
+{: .no_toc .text-delta}
+
+1. TOC
+{:toc}
-...
# The API
-The base URL is: https://api.delphi.cmu.edu/epidata/fluview_clinical/
+The base URL is:
-See [this documentation](README.md) for details on specifying epiweeks, dates, and lists.
## Parameters
@@ -32,19 +48,20 @@ See [this documentation](README.md) for details on specifying epiweeks, dates, a
| Parameter | Description | Type |
| --- | --- | --- |
-| `epiweeks` | epiweeks | `list` of epiweeks |
-| `regions` | regions | `list` of [region](https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt) labels |
+| `epiweeks` | epiweeks (see [Date Formats](date_formats.html)) | `list` of epiweeks |
+| `regions` | regions | `list` of region labels: `nat`, states, `hhs1`-`hhs10`, `cen1`-`cen9` (see [Geographic Codes](geographic_codes.html#us-regions-and-states)) |
### Optional
| Parameter | Description | Type |
|-----------|--------------------------------------------|--------------------|
-| `issues` | issues | `list` of epiweeks |
+| `issues` | issues (see [Date Formats](date_formats.html)) | `list` of epiweeks |
| `lag` | # weeks between each epiweek and its issue | integer |
-Notes:
-- If both `issues` and `lag` are specified, only `issues` is used.
-If neither is specified, the current issues are used.
+{: .note}
+> **Notes:**
+> - If both `issues` and `lag` are specified, only `issues` is used.
+> - If neither is specified, the current issues are used.
## Response
@@ -52,89 +69,142 @@ If neither is specified, the current issues are used.
|------------------------------|-----------------------------------------------------------------|------------------|
| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
| `epidata` | list of results | array of objects |
-| `epidata[].release_date` | | string |
-| `epidata[].region` | | string |
-| `epidata[].issue` | | integer |
-| `epidata[].epiweek` | | integer |
-| `epidata[].lag` | | integer |
-| `epidata[].total_specimens` | | integer |
-| `epidata[].total_a` | | integer |
-| `epidata[].total_b` | | integer |
-| `epidata[].percent_positive` | | float |
-| `epidata[].percent_a` | | float |
-| `epidata[].percent_b` | | float |
+| `epidata[].release_date` | date when data was released | string |
+| `epidata[].region` | region identifier | string |
+| `epidata[].issue` | epiweek of publication | integer |
+| `epidata[].epiweek` | epiweek for which data is valid | integer |
+| `epidata[].lag` | number of weeks between epiweek and issue | integer |
+| `epidata[].total_specimens` | total number of specimens tested | integer |
+| `epidata[].total_a` | total specimens positive for influenza A | integer |
+| `epidata[].total_b` | total specimens positive for influenza B | integer |
+| `epidata[].percent_positive` | percentage of specimens testing positive for influenza | float |
+| `epidata[].percent_a` | percentage of specimens testing positive for influenza A | float |
+| `epidata[].percent_b` | percentage of specimens testing positive for influenza B | float |
| `message` | `success` or error message | string |
# Example URLs
### FluView Clinical on 2020w01 (national)
-https://api.delphi.cmu.edu/epidata/fluview_clinical/?regions=nat&epiweeks=202001
+
```json
{
"result": 1,
"epidata": [
{
- "release_date": "2020-04-10",
+ "release_date": "2021-10-08",
"region": "nat",
- "issue": 202014,
+ "issue": 202139,
"epiweek": 202001,
- "lag": 13,
- "total_specimens": 64980,
- "total_a": 5651,
- "total_b": 9647,
- "percent_positive": 23.5426,
- "percent_a": 8.69652,
- "percent_b": 14.8461
- },
- ...
+ "lag": 91,
+ "total_specimens": 65177,
+ "total_a": 5645,
+ "total_b": 9664,
+ "percent_positive": 23.4883,
+ "percent_a": 8.66103,
+ "percent_b": 14.8273
+ }
],
"message": "success"
}
```
-
# Code Samples
-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).
-The following samples show how to import the library and fetch national FluView Clinical data for epiweeks `201940` and `202001-202010` (11 weeks total).
+Libraries are available for [R](https://cmu-delphi.github.io/epidatr/) and [Python](https://cmu-delphi.github.io/epidatpy/).
+The following samples show how to import the library and fetch national FluView Clinical data for epiweeks `201601-201701`.
+
+
+
-### JavaScript (in a web browser)
+
-````html
-
-
-
-
-````
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+res = Epidata.fluview_clinical(['nat'], [Epidata.range(201601, 201701)])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
-### Python
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_fluview_clinical(regions = "nat", epiweeks = epirange(201601, 201701))
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
-Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+Place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.fluview_clinical(['nat'], [201940, Epidata.range(202001, 202010)])
+res = Epidata.fluview_clinical(['nat'], [Epidata.range(201601, 201701)])
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
-### R
+
-````R
-# Import
-source('delphi_epidata.R')
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$fluview_clinical(list('nat'), list(201940, Epidata$range(202001, 202010)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$fluview_clinical(regions = list("nat"), epiweeks = list(Epidata$range(201601, 201701)))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+ ```html
+
+
+
+
+ ```
+
+
+
+
+
+
+
+```python
+# Import
+from epidatpy import EpiDataContext
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_fluview_meta()
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_fluview_meta()
+print(res)
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_gft(locations='nat', epiweeks=EpiRange(201501, 201510))
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_gft(locations = 'nat', epiweeks = epirange(201501, 201510))
+print(res)
+```
+
-### Python
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.gft(['nat'], [201440, Epidata.range(201501, 201510)])
+res = Epidata.gft(['nat'], Epidata.range(201501, 201510))
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
-### R
+
-````R
-# Import
-source('delphi_epidata.R')
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$gft(list('nat'), list(201440, Epidata$range(201501, 201510)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$gft(locations = list("nat"), epiweeks = Epidata$range(201501, 201510))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+Click to expand full list of valid queries
+
+* `/m/0cycc`
+* `influenza type a`
+* `flu duration`
+* `flu fever`
+* `treating flu`
+* `fever flu`
+* `flu recovery`
+* `braun thermoscan`
+* `oscillococcinum`
+* `treating the flu`
+* `cold or flu`
+* `flu versus cold`
+* `flu remedies`
+* `contagious flu`
+* `type a influenza`
+* `flu or cold`
+* `duration of flu`
+* `cold versus flu`
+* `flu cough`
+* `flu headache`
+* `thermoscan`
+* `influenza incubation period`
+* `flu lasts`
+* `length of flu`
+* `flu stomach`
+* `cold vs flu`
+* `flu and fever`
+* `getting over the flu`
+* `influenza a`
+* `treatment for flu`
+* `flu length`
+* `treatment for the flu`
+* `influenza symptoms`
+* `over the counter flu`
+* `flu complications`
+* `cold and flu symptoms`
+* `influenza incubation`
+* `treatment of flu`
+* `human temperature`
+* `low body`
+* `flu contagious`
+* `robitussin ac`
+* `flu how long`
+* `ear thermometer`
+* `flu contagious period`
+* `treat flu`
+* `cough flu`
+* `low body temperature`
+* `expectorant`
+* `flu and cold`
+* `rapid flu`
+* `flu vs. cold`
+* `how to treat the flu`
+* `how long does the flu last?`
+* `viral pneumonia`
+* `flu in kids`
+* `type a flu`
+* `influenza treatment`
+* `fighting the flu`
+* `flu relief`
+* `treat the flu`
+* `flu medicine`
+* `dangerous fever`
+* `what is influenza`
+* `tussin`
+* `low body temp`
+* `flu care`
+* `flu in infants`
+* `flu dizziness`
+* `feed a fever`
+* `flu vs cold`
+* `flu vomiting`
+* `bacterial pneumonia`
+* `flu activity`
+* `flu chills`
+* `anas barbariae`
+* `flu germs`
+* `tylenol cold`
+* `how to get over the flu`
+* `flu in children`
+* `influenza a and b`
+* `duration of the flu`
+* `cold symptoms`
+* `flu report`
+* `rapid flu test`
+* `flu relapse`
+* `get over the flu`
+* `flu during pregnancy`
+* `flu recovery time`
+* `cure for flu`
+* `tamiflu and breastfeeding`
+* `flu chest pain`
+* `flu treatment`
+* `flu nausea`
+* `remedies for the flu`
+* `tamiflu in pregnancy`
+* `side effects of tamiflu`
+* `how to treat flu`
+* `viral bronchitis`
+* `flu how long contagious`
+* `flu remedy`
+
+
## Response
-| Field | Description | Type |
-|-----------|-----------------------------------------------------------------|------------------|
-| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
-| `epidata` | list of results | array of objects |
-| ... | ... | ... |
-| `message` | `success` or error message | string |
+| Field | Description | Type |
+|-----------------------|-----------------------------------------------------------------|------------------|
+| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
+| `epidata` | list of results | array of objects |
+| `epidata[].location` | location label | string |
+| `epidata[].epiweek` | epiweek | integer |
+| `epidata[].query` | search query | string |
+| `epidata[].value` | search volume | float |
+| `message` | `success` or error message | string |
# Example URLs
-
+### Google Health Trends for "how to get over the flu" on 2015w01 (US)
+
+
+```json
+{
+ "result": 1,
+ "epidata": [
+ {
+ "location": "US",
+ "epiweek": 201501,
+ "query": "flu",
+ "value": 9.113
+ }
+ ],
+ "message": "success"
+}
+```
# Code Samples
-
+Libraries are available for [R](https://cmu-delphi.github.io/epidatr/) and [Python](https://cmu-delphi.github.io/epidatpy/).
+The following samples show how to import the library and fetch GHT data for "how to get over the flu" in the US for epiweek `201501`.
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.ght('auth_token', ['US'], [201501], 'how to get over the flu')
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_ght(auth = 'auth_token', locations = 'US', epiweeks = 201501,
+ query = "how to get over the flu")
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.ght('auth_token', ['US'], [201501], 'how to get over the flu')
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$ght(auth = "auth_token", locations = list("US"), epiweeks = list(201501), query = "how to get over the flu")
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_nowcast(locations=['nat'], epiweeks=EpiRange(202001, 202010))
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_nowcast(locations = 'nat', epiweeks = epirange(202001, 202010))
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.nowcast(['nat'], [201940, Epidata.range(202001, 202010)])
+res = Epidata.nowcast(['nat'], Epidata.range(202001, 202010))
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
-### R
+
-````R
-# Import
-source('delphi_epidata.R')
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$nowcast(list('nat'), list(201940, Epidata$range(202001, 202010)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$nowcast(locations = list("nat"), epiweeks = Epidata$range(202001, 202010))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_kcdc_ili(regions=['ROK'], epiweeks=[202001, 202002])
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_kcdc_ili(regions = 'ROK', epiweeks = c(202001, 202002))
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.kcdc_ili(['ROK'], [202001, 202002])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$kcdc_ili(regions = list("ROK"), epiweeks = list(202001, 202002))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_nidss_dengue(locations=['nationwide'], epiweeks=EpiRange(201501, 201510))
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_nidss_dengue(locations = 'nationwide', epiweeks = epirange(201501, 201510))
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.nidss_dengue(['nationwide'], [201440, Epidata.range(201501, 201510)])
+res = Epidata.nidss_dengue(['nationwide'], Epidata.range(201501, 201510))
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
+# Source and Licensing
-### R
+The full text of the NIDSS Dengue license information is available on the Taiwan Digital Development Department's [website](https://data.gov.tw/license).
+
-````R
-# Import
-source('delphi_epidata.R')
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$nidss_dengue(list('nationwide'), list(201440, Epidata$range(201501, 201510)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$nidss_dengue(regions = list("nationwide"), epiweeks = Epidata$range(201501, 201510))
+print(res$message)
+print(length(res$epidata))
+```
+
-# Source and Licensing
+
+
+
+
+```html
+
+
+
+
+```
+
-The full text of the NIDSS Dengue license information is available on the Taiwan Digital Development Department's [website](https://data.gov.tw/license).
\ No newline at end of file
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_nidss_flu(regions=['nationwide'], epiweeks=EpiRange(201501, 201510))
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_nidss_flu(regions = 'nationwide', epiweeks = epirange(201501, 201510))
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.nidss_flu(['nationwide'], [201440, Epidata.range(201501, 201510)])
+res = Epidata.nidss_flu(['nationwide'], Epidata.range(201501, 201510))
print(res['result'], res['message'], len(res['epidata']))
-````
+```
-### R
+# Source and Licensing
-````R
-# Import
-source('delphi_epidata.R')
+The full text of the NIDSS Flu license information is available on the Taiwan Digital Development Department's [website](https://data.gov.tw/license).
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$nidss_flu(list('nationwide'), list(201440, Epidata$range(201501, 201510)))
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$nidss_flu(regions = list("nationwide"), epiweeks = Epidata$range(201501, 201510))
+print(res$message)
+print(length(res$epidata))
+```
+
-# Source and Licensing
+
+
+
+
+```html
+
+
+
+
+```
+
-The full text of the NIDSS Flu license information is available on the Taiwan Digital Development Department's [website](https://data.gov.tw/license).
\ No newline at end of file
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pvt_norostat(auth='auth_token', locations=['Minnesota, Ohio, Oregon, Tennessee, and Wisconsin'], epiweeks=[201501])
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_norostat(auth = 'auth_token', locations = 'Minnesota, Ohio, Oregon, Tennessee, and Wisconsin', epiweeks = 201501)
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.norostat('auth_token', ['Minnesota, Ohio, Oregon, Tennessee, and Wisconsin'], [201501])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$norostat(auth = "auth_token", locations = list("Minnesota, Ohio, Oregon, Tennessee, and Wisconsin"), epiweeks = list(201501))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pvt_meta_norostat(auth='auth_token')
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_meta_norostat(auth = 'auth_token')
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.meta_norostat('auth_token')
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$meta_norostat(auth = "auth_token")
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
*Note: Data availability varies by country.* |
+| **Temporal Granularity** | Weekly (Epiweek) |
+| **Reporting Cadence** | Inactive - No longer updated since 2020w31 |
+| **Temporal Scope Start** | 2014w01 |
+| **License** | This was scraped from a publicly-accessible website, but no explicit license terms were found. |
+
+## Overview
+{: .no_toc}
+
+This data source provides weekly dengue case counts for countries and territories in the Americas, as reported by the Pan American Health Organization (PAHO).
General topics not specific to any particular endpoint are discussed in the
[API overview](README.md). Such topics include:
[contributing](README.md#contributing), [citing](README.md#citing), and
[data licensing](README.md#data-licensing).
-## PAHO Dengue Data
+## Table of contents
+{: .no_toc .text-delta}
+
+1. TOC
+{:toc}
+
-...
# The API
-The base URL is: https://api.delphi.cmu.edu/epidata/paho_dengue/
+The base URL is:
-See [this documentation](README.md) for details on specifying epiweeks, dates, and lists.
## Parameters
### Required
-
+| Parameter | Description | Type |
+| --- | --- | --- |
+| `epiweeks` | epiweeks (see [Date Formats](date_formats.html)) | `list` of epiweeks |
+| `regions` | regions | `list` of region labels (see [Geographic Codes](geographic_codes.html#paho-dengue)) |
## Response
-| Field | Description | Type |
-|-----------|-----------------------------------------------------------------|------------------|
-| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
-| `epidata` | list of results | array of objects |
-| ... | ... | ... |
-| `message` | `success` or error message | string |
+| Field | Description | Type |
+|------------------------------|-----------------------------------------------------------------|------------------|
+| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
+| `epidata` | list of results | array of objects |
+| `epidata[].release_date` | date when data was released | date (YYYY-MM-DD)|
+| `epidata[].region` | region label (ISO 3166-1 alpha-2 code) | string |
+| `epidata[].serotype` | dengue serotype information | string |
+| `epidata[].issue` | epiweek when data was issued | integer |
+| `epidata[].epiweek` | epiweek for the data point | integer |
+| `epidata[].lag` | number of weeks between epiweek and issue | integer |
+| `epidata[].total_pop` | total population (in thousands) | integer |
+| `epidata[].num_dengue` | total number of dengue cases | integer |
+| `epidata[].num_severe` | number of severe dengue cases | integer |
+| `epidata[].num_deaths` | number of dengue-related deaths | integer |
+| `epidata[].incidence_rate` | incidence rate per 100,000 population | float |
+| `message` | `success` or error message | string |
# Example URLs
-
+### PAHO Dengue on 2015w01 (Canada)
+
+
+```json
+{
+ "result": 1,
+ "epidata": [
+ {
+ "release_date": "2020-08-07",
+ "region": "CA",
+ "serotype": " ",
+ "issue": 202032,
+ "epiweek": 201501,
+ "lag": 291,
+ "total_pop": 0,
+ "num_dengue": 0,
+ "num_severe": 0,
+ "num_deaths": 0,
+ "incidence_rate": 0.0
+ }
+ ],
+ "message": "success"
+}
+```
# Code Samples
-
+Libraries are available for [R](https://cmu-delphi.github.io/epidatr/) and [Python](https://cmu-delphi.github.io/epidatpy/).
+The following samples show how to import the library and fetch PAHO Dengue data for Canada for epiweek `201501`.
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_paho_dengue(regions=['ca'], epiweeks=[201501])
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_paho_dengue(regions = 'ca', epiweeks = 201501)
+print(res)
+```
+
+
+
+
+
+
+
+Place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.paho_dengue(['ca'], [201501])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$paho_dengue(regions = list("ca"), epiweeks = list(201501))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pvt_quidel(auth='auth_token', locations=['hhs1'], epiweeks=EpiRange(201535, 202001))
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_quidel(auth = 'auth_token', locations = 'hhs1', epiweeks = epirange(201535, 202001))
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.quidel('auth_token', ['hhs1'], Epidata.range(201535, 202001))
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$quidel(auth = "auth_token", locations = list("hhs1"), epiweeks = Epidata$range(201535, 202001))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+
+
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
+
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pvt_twitter(auth='auth_token', locations=['nat'], time_type="week", time_values=[201501])
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pvt_twitter(auth = 'auth_token', locations = 'nat',
+ time_type = "week", time_values = 201501)
+print(res)
+```
+
+
+
+
+
+
+
+Optionally install the package using pip(env):
+```bash
+pip install delphi-epidata
+```
+
+Otherwise, place `delphi_epidata.py` from this repo next to your python script.
+
+```python
+# Import
+from delphi_epidata import Epidata
+# Fetch data
+res = Epidata.twitter('auth_token', ['nat'], time_type="week", time_values=[201501])
+print(res['result'], res['message'], len(res['epidata']))
+```
+
+
+
+
+Place `delphi_epidata.R` from this repo next to your R script.
+
+```R
+source("delphi_epidata.R")
+# Fetch data
+res <- Epidata$twitter(auth = "auth_token", locations = list("nat"), time_type = "week", time_values = list(201501))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
+Click to expand full list of articles
+
+| Article Name |
+|---|
+| amantadine |
+| antiviral_drugs |
+| avian_influenza |
+| canine_influenza |
+| cat_flu |
+| chills |
+| common_cold |
+| cough |
+| equine_influenza |
+| fatigue_(medical) |
+| fever |
+| flu_season |
+| gastroenteritis |
+| headache |
+| hemagglutinin_(influenza) |
+| human_flu |
+| influenza |
+| influenzalike_illness |
+| influenzavirus_a |
+| influenzavirus_c |
+| influenza_a_virus |
+| influenza_a_virus_subtype_h10n7 |
+| influenza_a_virus_subtype_h1n1 |
+| influenza_a_virus_subtype_h1n2 |
+| influenza_a_virus_subtype_h2n2 |
+| influenza_a_virus_subtype_h3n2 |
+| influenza_a_virus_subtype_h3n8 |
+| influenza_a_virus_subtype_h5n1 |
+| influenza_a_virus_subtype_h7n2 |
+| influenza_a_virus_subtype_h7n3 |
+| influenza_a_virus_subtype_h7n7 |
+| influenza_a_virus_subtype_h7n9 |
+| influenza_a_virus_subtype_h9n2 |
+| influenza_b_virus |
+| influenza_pandemic |
+| influenza_prevention |
+| influenza_vaccine |
+| malaise |
+| myalgia |
+| nasal_congestion |
+| nausea |
+| neuraminidase_inhibitor |
+| orthomyxoviridae |
+| oseltamivir |
+| paracetamol |
+| rhinorrhea |
+| rimantadine |
+| shivering |
+| sore_throat |
+| swine_influenza |
+| viral_neuraminidase |
+| viral_pneumonia |
+| vomiting |
+| zanamivir |
+
+
+
-Note:
-- Only one of `dates` and `epiweeks` is required. If both are provided, `epiweeks` is ignored.
### Optional
@@ -50,25 +126,31 @@ Note:
|-----------|-------------|------------------------|
| `hours` | hours | `list` of hours (0-23) |
+{: .note}
+> **Notes:**
+> - Only one of `dates` and `epiweeks` is required. If both are provided, `epiweeks` is ignored.
+> - `dates`, `epiweeks`, and `hours` are `None` by default.
+> - `language` is `en` by default.
+
## Response
| Field | Description | Type |
|---------------------|-----------------------------------------------------------------|------------------|
| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
| `epidata` | list of results | array of objects |
-| `epidata[].article` | | string |
-| `epidata[].count` | | integer |
-| `epidata[].total` | | integer |
-| `epidata[].hour` | hour (-1 if `hour` not used) | integer |
+| `epidata[].article` | Wikipedia article name | string |
+| `epidata[].count` | number of pageviews | integer |
+| `epidata[].total` | total pageviews | integer |
+| `epidata[].hour` | hour (-1 if `hour` not used) | integer |
| `epidata[].date` | date (yyyy-MM-dd) (only included if `date` used) | string |
| `epidata[].epiweek` | epiweek (only included if `epiweek` used) | integer |
-| `epidata[].value` | | float |
+| `epidata[].value` | normalized pageview count | float |
| `message` | `success` or error message | string |
# Example URLs
### Wikipedia Access article "influenza" on 2020w01
-https://api.delphi.cmu.edu/epidata/wiki/?language=en&articles=influenza&epiweeks=202001
+
```json
{
@@ -88,7 +170,7 @@ https://api.delphi.cmu.edu/epidata/wiki/?language=en&articles=influenza&epiweeks
```
### Wikipedia Access article "influenza" on date 2020-01-01
-https://api.delphi.cmu.edu/epidata/wiki/?language=en&articles=influenza&dates=20200101
+
```json
{
@@ -109,52 +191,101 @@ https://api.delphi.cmu.edu/epidata/wiki/?language=en&articles=influenza&dates=20
# Code Samples
-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).
-The following samples show how to import the library and fetch national Wikipedia Access data for article "influenza" on
-epiweeks `201940` and `202001-202010` (11 weeks total) for hours 0 and 12 in English.
+Libraries are available for [R](https://cmu-delphi.github.io/epidatr/) and [Python](https://cmu-delphi.github.io/epidatpy/).
+The following samples show how to import the library and fetch Wikipedia Access data for article "influenza" in English for epiweeks `202001-202010` (10 weeks total) and hours 0 and 12.
-
+
+
-````html
-
-
-
-
-````
+
+
+Install the package using pip:
+```bash
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
+```
-### Python
+```python
+# Import
+from epidatpy import CovidcastEpidata, EpiDataContext, EpiRange
+# Fetch data
+epidata = EpiDataContext()
+res = epidata.pub_wiki(articles=['influenza'], time_values=EpiRange(202001, 202010), time_type='week', language='en', hours=[0, 12])
+print(res)
+```
+
+
+
+
+```R
+library(epidatr)
+# Fetch data
+res <- pub_wiki(articles = "influenza", time_values = epirange(202001, 202010),
+ time_type = "week", language = "en", hours = c(0, 12))
+print(res)
+```
+
+
+
+
+
+
Optionally install the package using pip(env):
-````bash
+```bash
pip install delphi-epidata
-````
+```
Otherwise, place `delphi_epidata.py` from this repo next to your python script.
-````python
+```python
# Import
from delphi_epidata import Epidata
# Fetch data
-res = Epidata.wiki(['influenza'], None, [201940, Epidata.range(202001, 202010)], [0, 12])
+res = Epidata.wiki(['influenza'], Epidata.range(202001, 202010), {'time_type': 'week', 'language': 'en', 'hours': [0, 12]})
print(res['result'], res['message'], len(res['epidata']))
-````
+```
+
-Note:
-- `dates`, `epiweeks`, and `hours` are `None` by default.
-- `language` is `en` by default.
+
-### R
+Place `delphi_epidata.R` from this repo next to your R script.
-````R
-# Import
-source('delphi_epidata.R')
+```R
+source("delphi_epidata.R")
# Fetch data
-res <- Epidata$wiki(list('nat'), NULL, list(201940, Epidata$range(202001, 202010)), list(0, 12), 'en')
-cat(paste(res$result, res$message, length(res$epidata), "\n"))
-````
+res <- Epidata$wiki(articles = list("influenza"), time_values = Epidata$range(202001, 202010), time_type = "week", options = list(language = "en", hours = list(0, 12)))
+print(res$message)
+print(length(res$epidata))
+```
+
+
+
+
+
+```html
+
+
+
+
+```
+
+
+
`
+2. **Header:** `