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51 | 51 | toc: true
|
52 | 52 | ---
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53 | 53 |
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54 |
| -<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script> |
55 | 54 |
|
56 | 55 | <div id="TOC">
|
57 | 56 | <ul>
|
58 |
| -<li><a href="#purpose-of-the-api">Purpose of the API</a></li> |
59 |
| -<li><a href="#unique-data-sources">Unique Data Sources</a></li> |
60 |
| -<li><a href="#tracking-observations-and-revisions">Tracking Observations and Revisions</a></li> |
61 |
| -<li><a href="#accessing-the-api">Accessing the API</a></li> |
62 |
| -<li><a href="#putting-the-api-to-work">Putting the API to Work</a></li> |
| 57 | +<li><a href="#purpose-of-the-api" id="toc-purpose-of-the-api">Purpose of the API</a></li> |
| 58 | +<li><a href="#unique-data-sources" id="toc-unique-data-sources">Unique Data Sources</a></li> |
| 59 | +<li><a href="#tracking-observations-and-revisions" id="toc-tracking-observations-and-revisions">Tracking Observations and Revisions</a></li> |
| 60 | +<li><a href="#accessing-the-api" id="toc-accessing-the-api">Accessing the API</a></li> |
| 61 | +<li><a href="#putting-the-api-to-work" id="toc-putting-the-api-to-work">Putting the API to Work</a></li> |
63 | 62 | </ul>
|
64 | 63 | </div>
|
65 | 64 |
|
@@ -294,182 +293,7 @@ <h2>Tracking Observations and Revisions</h2>
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294 | 293 | knitr::kable("html", digits = 2,
|
295 | 294 | col.names = c("Test date", "Positivity rate (%)", "Sample size",
|
296 | 295 | "Issued on", "Lag (days)"))</code></pre>
|
297 |
| -<table> |
298 |
| -<thead> |
299 |
| -<tr> |
300 |
| -<th style="text-align:left;"> |
301 |
| -Test date |
302 |
| -</th> |
303 |
| -<th style="text-align:right;"> |
304 |
| -Positivity rate (%) |
305 |
| -</th> |
306 |
| -<th style="text-align:right;"> |
307 |
| -Sample size |
308 |
| -</th> |
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| -<th style="text-align:left;"> |
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| -Issued on |
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| -</th> |
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| -<th style="text-align:right;"> |
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| -Lag (days) |
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| -</th> |
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| -</tr> |
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| -</thead> |
317 |
| -<tbody> |
318 |
| -<tr> |
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| -<td style="text-align:left;"> |
320 |
| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -1.01 |
324 |
| -</td> |
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| -<td style="text-align:right;"> |
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| -198 |
327 |
| -</td> |
328 |
| -<td style="text-align:left;"> |
329 |
| -2020-08-06 |
330 |
| -</td> |
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| -<td style="text-align:right;"> |
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| -5 |
333 |
| -</td> |
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| -</tr> |
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| -<tr> |
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| -<td style="text-align:left;"> |
337 |
| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -0.97 |
341 |
| -</td> |
342 |
| -<td style="text-align:right;"> |
343 |
| -206 |
344 |
| -</td> |
345 |
| -<td style="text-align:left;"> |
346 |
| -2020-08-07 |
347 |
| -</td> |
348 |
| -<td style="text-align:right;"> |
349 |
| -6 |
350 |
| -</td> |
351 |
| -</tr> |
352 |
| -<tr> |
353 |
| -<td style="text-align:left;"> |
354 |
| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
357 |
| -1.41 |
358 |
| -</td> |
359 |
| -<td style="text-align:right;"> |
360 |
| -284 |
361 |
| -</td> |
362 |
| -<td style="text-align:left;"> |
363 |
| -2020-08-10 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -9 |
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| -</td> |
368 |
| -</tr> |
369 |
| -<tr> |
370 |
| -<td style="text-align:left;"> |
371 |
| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -1.38 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -290 |
378 |
| -</td> |
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| -<td style="text-align:left;"> |
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| -2020-08-12 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -11 |
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| -</td> |
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| -</tr> |
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| -<tr> |
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| -<td style="text-align:left;"> |
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| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -1.33 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -377 |
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| -</td> |
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| -<td style="text-align:left;"> |
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| -2020-08-16 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -15 |
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| -</td> |
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| -</tr> |
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| -<tr> |
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| -<td style="text-align:left;"> |
405 |
| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -1.53 |
409 |
| -</td> |
410 |
| -<td style="text-align:right;"> |
411 |
| -459 |
412 |
| -</td> |
413 |
| -<td style="text-align:left;"> |
414 |
| -2020-08-19 |
415 |
| -</td> |
416 |
| -<td style="text-align:right;"> |
417 |
| -18 |
418 |
| -</td> |
419 |
| -</tr> |
420 |
| -<tr> |
421 |
| -<td style="text-align:left;"> |
422 |
| -2020-08-01 |
423 |
| -</td> |
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| -<td style="text-align:right;"> |
425 |
| -1.47 |
426 |
| -</td> |
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| -<td style="text-align:right;"> |
428 |
| -477 |
429 |
| -</td> |
430 |
| -<td style="text-align:left;"> |
431 |
| -2020-08-20 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -19 |
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| -</td> |
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| -</tr> |
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| -<tr> |
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| -<td style="text-align:left;"> |
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| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -1.46 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -479 |
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| -</td> |
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| -<td style="text-align:left;"> |
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| -2020-08-26 |
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| -</td> |
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| -<td style="text-align:right;"> |
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| -25 |
452 |
| -</td> |
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| -</tr> |
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| -<tr> |
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| -<td style="text-align:left;"> |
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| -2020-08-01 |
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| -</td> |
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| -<td style="text-align:right;"> |
459 |
| -1.36 |
460 |
| -</td> |
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| -<td style="text-align:right;"> |
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| -513 |
463 |
| -</td> |
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| -<td style="text-align:left;"> |
465 |
| -2020-08-30 |
466 |
| -</td> |
467 |
| -<td style="text-align:right;"> |
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| -29 |
469 |
| -</td> |
470 |
| -</tr> |
471 |
| -</tbody> |
472 |
| -</table> |
| 296 | +<p><em>November 2023 update: Quidel data is no longer publicly available, so the table generated by the code chunk above has been removed.</em></p> |
473 | 297 | <p>Many data sources are subject to revisions:</p>
|
474 | 298 | <ul>
|
475 | 299 | <li>Case and death counts are frequently corrected or adjusted by authorities.</li>
|
@@ -556,13 +380,15 @@ <h2>Accessing the API</h2>
|
556 | 380 | <pre class="python"><code>import covidcast
|
557 | 381 | from datetime import date
|
558 | 382 | import matplotlib.pyplot as plt
|
| 383 | +import os |
| 384 | + |
| 385 | +covidcast.use_api_key(os.environ['API_KEY']) # for more on API keys, see: https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html |
559 | 386 |
|
560 | 387 | data = covidcast.signal("fb-survey", "smoothed_hh_cmnty_cli",
|
561 | 388 | date(2020, 9, 8), date(2020, 9, 8),
|
562 | 389 | geo_type="state")
|
563 | 390 | covidcast.plot_choropleth(data, figsize=(7, 5))
|
564 | 391 | plt.title("% who know someone who is sick, Sept 8, 2020")</code></pre>
|
565 |
| -<p><img src="/blog/2020-08-28-api_files/figure-html/python-data-1.svg" /><!-- --></p> |
566 | 392 | <p>Each package’s documentation gives numerous other examples of pulling, plotting,
|
567 | 393 | and mapping data from our API. (Note that the Export Data feature in the map can
|
568 | 394 | also show you example R or Python code to download any signal from the map.)
|
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