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Merged
merged 36 commits into from
May 31, 2024
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a4bcf1c
add R script for updating fields in signal spreadsheet
nmdefries May 7, 2024
72b7c3d
Update signal_spreadsheet_updater.R
tinatownes May 7, 2024
d338f43
remove column name change TODOs
nmdefries May 7, 2024
71bbe3e
info about censoring
nmdefries May 7, 2024
cc5ee22
clean up censor section
nmdefries May 7, 2024
903e79c
add backfill/lag tool
nmdefries May 7, 2024
d068b3e
add missingness
nmdefries May 8, 2024
6a3733d
save output
nmdefries May 8, 2024
a29cee3
cleanup
nmdefries May 8, 2024
b671c36
updates to DUA, Quidel
tinatownes May 9, 2024
e1582fa
Merge branch 'ndefries/signal-spreadsheet-updater-script' of https://…
tinatownes May 9, 2024
dca3427
Revert "updates to DUA, Quidel"
nmdefries May 9, 2024
2f76a76
merge dua changes
nmdefries May 9, 2024
71db9d6
fb dua clarification
nmdefries May 9, 2024
120e4e5
cleanup
nmdefries May 9, 2024
99f9292
intro to script
nmdefries May 9, 2024
8306572
safegraph use restrictions
nmdefries May 9, 2024
b49fe31
Merge branch 'dev' into ndefries/signal-spreadsheet-updater-script
nmdefries May 9, 2024
3814899
updated Facebook DUA line 1008 with clarification
tinatownes May 10, 2024
13d0135
quidel signal-specific missingness
nmdefries May 10, 2024
cf5a440
quidel TODO
nmdefries May 10, 2024
9b5c16b
quidel TODO
nmdefries May 10, 2024
999273d
for quidel signals, use existing start/end times
nmdefries May 28, 2024
96da3bb
verify quidel geo availability
nmdefries May 28, 2024
4618d93
Merge pull request #1455 from cmu-delphi/bot/sync-main-dev
melange396 May 29, 2024
e71211b
note geos we created in separate col
nmdefries May 29, 2024
59d3734
generalize coalesce for start/end dates
nmdefries May 29, 2024
73d78cd
quidel revision cadence and TODO
nmdefries May 29, 2024
70e9816
chore: update docs
nmdefries May 29, 2024
70b99f5
Merge pull request #1457 from cmu-delphi/bot/update-docs
melange396 May 29, 2024
7eadc13
state epidatr is ready
nmdefries May 29, 2024
921d0d4
Merge pull request #1430 from cmu-delphi/ndefries/signal-spreadsheet-…
nmdefries May 29, 2024
060c097
reorder clients by importance
nmdefries May 30, 2024
058489f
Merge pull request #1458 from cmu-delphi/ndefries/epidatr-ready-text
nmdefries May 30, 2024
3673ac9
fix: Python client logger import (#1460)
dshemetov May 31, 2024
573fdb5
chore: release delphi-epidata 4.1.23
melange396 May 31, 2024
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 4.1.22
current_version = 4.1.23
commit = False
tag = False

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2 changes: 1 addition & 1 deletion dev/local/setup.cfg
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[metadata]
name = Delphi Development
version = 4.1.22
version = 4.1.23

[options]
packages =
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60 changes: 37 additions & 23 deletions docs/api/client_libraries.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,39 +8,39 @@ nav_order: 1

For anyone looking for COVIDCast data, please visit our [COVIDCast Libraries](covidcast_clients.md).

We are currently working on fully-featured Epidata clients for R and Python. They are not ready
for release yet, but you can track our development progress and help us test them out at:
A full-featured Epidata client for R is available at
[epidatr](https://github.com/cmu-delphi/epidatr) and
[also on CRAN](https://cran.r-project.org/web/packages/epidatr/index.html).

* [epidatr](https://github.com/cmu-delphi/epidatr)
* [epidatpy](https://github.com/cmu-delphi/epidatpy)
We are currently working on a new full-featured Epidata client for Python. It is not ready
for release yet, but you can track our development progress and help us test it out at
[epidatpy](https://github.com/cmu-delphi/epidatpy).

In the meantime, minimalist Epidata clients remain available for
[JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js),
[Python](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.py),
[JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js),
and
[R](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.R).
[R (legacy)](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.R).
The following samples show how to import the library and fetch Delphi's COVID-19
Surveillance Streams from Facebook Survey CLI for county 06001 and days
Surveillance Streams from Facebook Survey CLI for county 06001, and days
`20200401` and `20200405-20200414` (11 days total).

### JavaScript (in a web browser)

The minimalist JavaScript client does not currently support API keys. If you need API key support in JavaScript, contact [email protected].
### R

````html
<!-- Imports -->
<script src="delphi_epidata.js"></script>
<!-- Fetch data -->
<script>
EpidataAsync.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401, EpidataAsync.range(20200405, 20200414)], '06001').then((res) => {
console.log(res.result, res.message, res.epidata != null ? res.epidata.length : 0);
});
</script>
````R
# [Optional] configure your API key, if desired
# Interactive. See https://cmu-delphi.github.io/epidatr/articles/epidatr.html#api-keys for details.
#save_api_key()
# Import
library(epidatr)
# Fetch data
res <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
time_values = c(20200401, 20200405:20200414))
cat(res)
````

### Python


Optionally install the [package from PyPI](https://pypi.org/project/delphi-epidata/) using pip(env):
````bash
pip install delphi-epidata
Expand All @@ -60,15 +60,29 @@ res = Epidata.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401,
print(res['result'], res['message'], len(res['epidata']))
````

### R
### JavaScript (in a web browser)

The minimalist JavaScript client does not currently support API keys. If you need API key support in JavaScript, contact [email protected].

````R
````html
<!-- Imports -->
<script src="delphi_epidata.js"></script>
<!-- Fetch data -->
<script>
EpidataAsync.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401, EpidataAsync.range(20200405, 20200414)], '06001').then((res) => {
console.log(res.result, res.message, res.epidata != null ? res.epidata.length : 0);
});
</script>
````

### R (legacy)

```R
# [Optional] configure your API key, if desired
#option('epidata.auth', <your API key>)
# Import
source('delphi_epidata.R')
# Fetch data
res <- Epidata$covidcast('fb-survey', 'smoothed_cli', 'day', 'county', list(20200401, Epidata$range(20200405, 20200414)), '06001')
cat(paste(res$result, res$message, length(res$epidata), "\n"))
````
```
2 changes: 1 addition & 1 deletion requirements.api.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
delphi_utils==0.3.15
delphi_utils
epiweeks==2.1.2
Flask==2.2.5
Flask-Limiter==3.3.0
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2 changes: 1 addition & 1 deletion requirements.dev.txt
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ aiohttp==3.9.4
black>=20.8b1
bump2version==1.0.1
covidcast==0.1.5
delphi_utils==0.3.15
delphi_utils
docker==6.0.1
dropbox==11.36.0
freezegun==1.2.2
Expand Down
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