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‎content/blog/2015-07-23-template-post.html

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toc: true
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---
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<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
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<div id="TOC">
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<ul>
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<li><a href="#including-plots" id="toc-including-plots">Including Plots</a>
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<li><a href="#including-plots">Including Plots</a>
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<ul>
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<li><a href="#wide-figure" id="toc-wide-figure">Wide Figure</a></li>
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<li><a href="#wide-figure">Wide Figure</a></li>
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</ul></li>
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<li><a href="#including-math" id="toc-including-math">Including Math</a></li>
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<li><a href="#metadata" id="toc-metadata">Metadata</a>
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<li><a href="#including-math">Including Math</a></li>
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<li><a href="#metadata">Metadata</a>
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<ul>
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<li><a href="#tags" id="toc-tags">Tags</a></li>
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<li><a href="#tags">Tags</a></li>
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</ul></li>
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<li><a href="#linking" id="toc-linking">Linking</a>
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<li><a href="#linking">Linking</a>
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<ul>
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<li><a href="#linking-to-other-pages-and-blog-posts" id="toc-linking-to-other-pages-and-blog-posts">Linking to other pages and blog posts:</a></li>
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<li><a href="#linking-to-the-api-doc" id="toc-linking-to-the-api-doc">Linking to the API doc:</a></li>
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<li><a href="#linking-to-other-pages-and-blog-posts">Linking to other pages and blog posts:</a></li>
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<li><a href="#linking-to-the-api-doc">Linking to the API doc:</a></li>
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</ul></li>
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</ul>
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</div>
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see <a href="http://rmarkdown.rstudio.com" class="uri">http://rmarkdown.rstudio.com</a>.</p>
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<p>You can embed an R code chunk like this:</p>
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<pre class="r"><code>summary(cars)
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## speed dist
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## Min. : 4.0 Min. : 2.00
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## 1st Qu.:12.0 1st Qu.: 26.00
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## Median :15.0 Median : 36.00
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## Mean :15.4 Mean : 42.98
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## 3rd Qu.:19.0 3rd Qu.: 56.00
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## speed dist
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## Min. : 4.0 Min. : 2.00
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## 1st Qu.:12.0 1st Qu.: 26.00
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## Median :15.0 Median : 36.00
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## Mean :15.4 Mean : 42.98
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## 3rd Qu.:19.0 3rd Qu.: 56.00
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## Max. :25.0 Max. :120.00
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fit &lt;- lm(dist ~ speed, data = cars)
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fit
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##
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##
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## Call:
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## lm(formula = dist ~ speed, data = cars)
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##
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##
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## Coefficients:
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## (Intercept) speed
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## (Intercept) speed
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## -17.579 3.932</code></pre>
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<div id="including-plots" class="section level2">
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<h2>Including Plots</h2>
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col = c(&#39;#0292D8&#39;, &#39;#F7EA39&#39;, &#39;#C4B632&#39;),
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init.angle = -50, border = NA
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)</code></pre>
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<div class="figure"><span style="display:block;" id="fig:pie"></span>
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<div class="figure"><span id="fig:pie"></span>
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<img src="/blog/2015-07-23-template-post_files/figure-html/pie-1.svg" alt="A fancy pie chart." width="672" />
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<p class="caption">
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Figure 1: A fancy pie chart.
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col = c(&#39;#0292D8&#39;, &#39;#F7EA39&#39;, &#39;#C4B632&#39;),
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init.angle = -50, border = NA
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)</code></pre>
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<div class="figure"><span style="display:block;" id="fig:wide-pie"></span>
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<div class="figure"><span id="fig:wide-pie"></span>
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<img src="/blog/2015-07-23-template-post_files/figure-html/wide-pie-1.svg" alt="A fancy pie chart." width="672" class="wide-figure" />
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<p class="caption">
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Figure 2: A fancy pie chart.

‎content/blog/2020-08-10-hello-world.html

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toc: true
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<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
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<div id="TOC">
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<ul>
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<li><a href="#a-little-bit-about-us" id="toc-a-little-bit-about-us">A Little Bit About Us</a></li>
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<li><a href="#our-mission-and-strategy" id="toc-our-mission-and-strategy">Our Mission and Strategy</a></li>
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<li><a href="#what-weve-been-up-to" id="toc-what-weve-been-up-to">What We’ve Been Up To</a></li>
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<li><a href="#a-little-bit-about-us">A Little Bit About Us</a></li>
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<li><a href="#our-mission-and-strategy">Our Mission and Strategy</a></li>
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<li><a href="#what-weve-been-up-to">What We’ve Been Up To</a></li>
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</ul>
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</div>
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‎content/blog/2020-08-26-fb-survey.html

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---
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<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
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<div id="TOC">
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<ul>
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<li><a href="#short-background" id="toc-short-background">Short Background</a></li>
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<li><a href="#why-run-these-surveys" id="toc-why-run-these-surveys">Why Run These Surveys?</a></li>
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<li><a href="#whats-in-the-survey" id="toc-whats-in-the-survey">What’s in the Survey?</a></li>
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<li><a href="#some-interesting-examples" id="toc-some-interesting-examples">Some Interesting Examples</a></li>
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<li><a href="#basic-correlation-analysis" id="toc-basic-correlation-analysis">Basic Correlation Analysis</a>
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<li><a href="#short-background">Short Background</a></li>
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<li><a href="#why-run-these-surveys">Why Run These Surveys?</a></li>
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<li><a href="#whats-in-the-survey">What’s in the Survey?</a></li>
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<li><a href="#some-interesting-examples">Some Interesting Examples</a></li>
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<li><a href="#basic-correlation-analysis">Basic Correlation Analysis</a>
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<ul>
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<li><a href="#correlations-sliced-by-time" id="toc-correlations-sliced-by-time">Correlations Sliced by Time</a></li>
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<li><a href="#correlations-sliced-by-county" id="toc-correlations-sliced-by-county">Correlations Sliced by County</a></li>
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<li><a href="#correlations-sliced-by-time">Correlations Sliced by Time</a></li>
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<li><a href="#correlations-sliced-by-county">Correlations Sliced by County</a></li>
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</ul></li>
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<li><a href="#whats-next-with-the-surveys" id="toc-whats-next-with-the-surveys">What’s Next with the Surveys</a></li>
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<li><a href="#whats-next-with-the-surveys">What’s Next with the Surveys</a></li>
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</ul>
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</div>
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title = &quot;Daily new confirmed COVID-19 cases per 100,000 people&quot;,
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range = c(0, 30), choro_params = list(subtitle = subtitle))
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grid.arrange(p1, p2, nrow = 1)</code></pre>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-3-1.svg" width="960" class="wide-figure" /></p>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-2-1.svg" width="960" class="wide-figure" /></p>
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<p>We generated these plots using our <a href="https://cmu-delphi.github.io/covidcast/covidcastR/">covidcast R
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package</a>.
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In all, fetching the data from our API and producing the heatmaps
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linetype = 2, size = 1, color = ggplot_colors[1]) +
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geom_vline(xintercept = as.numeric(as.Date(&quot;2020-06-25&quot;)),
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linetype = 2, size = 1, color = ggplot_colors[2])</code></pre>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-4-1.svg" width="576" /></p>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-3-1.svg" width="576" /></p>
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<p>This example, as with all code examples in this blog post, was produced using
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our <a href="https://cmu-delphi.github.io/covidcast/covidcastR/">covidcast R package</a>.</p>
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<p>A first glance reveals that the % CLI-in-community indicator
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p_list[[i]] = plot_one(geo_values[i], legend = FALSE)
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}
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do.call(grid.arrange, c(p_list, nrow = 5, ncol = 4))</code></pre>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-5-1.svg" width="960" class="wide-figure" /></p>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-4-1.svg" width="960" class="wide-figure" /></p>
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<p>The examples above are an informal way of looking
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at the <em>recall</em> of the % CLI-in-community signal.
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Of course, this is only one half of the story:
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subtitle = sprintf(&quot;Over all counties with at least %i cumulative cases&quot;,
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case_num), x = &quot;Date&quot;, y = &quot;Correlation&quot;) +
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theme_bw() + theme(legend.pos = &quot;bottom&quot;, legend.title = element_blank())</code></pre>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-6-1.svg" width="576" /></p>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-5-1.svg" width="576" /></p>
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<p>Another interesting observation is that the correlations from either indicator
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increase dramatically sometime around mid-June.
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subtitle = sprintf(&quot;Over all counties with at least %i cumulative cases&quot;,
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case_num), x = &quot;Date&quot;, y = &quot;Median abs deviation&quot;) +
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theme_bw()</code></pre>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-7-1.svg" width="576" /></p>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-6-1.svg" width="576" /></p>
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</div>
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<div id="correlations-sliced-by-county" class="section level3">
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<h3>Correlations Sliced by County</h3>
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subtitle = sprintf(&quot;Over all counties with at least %i cumulative cases&quot;,
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case_num), x = &quot;Correlation&quot;, y = &quot;Density&quot;) +
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theme_bw() + theme(legend.pos = &quot;bottom&quot;, legend.title = element_blank())</code></pre>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-8-1.svg" width="576" /></p>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-7-1.svg" width="576" /></p>
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<p>We can also examine choropleth maps of these correlations to learn
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where (geographically speaking) they’re high and where they’re not.
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As we can see from the maps below, the % CLI-in-community indicator
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p2 = plot(df_cor2, title = &quot;Correlation between % CLI-in-community and case rates&quot;,
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range = c(-1, 1), choro_col = cm.colors(10))
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grid.arrange(p1, p2, nrow = 1)</code></pre>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-9-1.svg" width="960" class="wide-figure" /></p>
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<p><img src="/blog/2020-08-26-fb-survey_files/figure-html/unnamed-chunk-8-1.svg" width="960" class="wide-figure" /></p>
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</div>
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<div id="whats-next-with-the-surveys" class="section level2">

‎content/blog/2020-08-28-api.html

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toc: true
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<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
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<div id="TOC">
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<ul>
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<li><a href="#purpose-of-the-api" id="toc-purpose-of-the-api">Purpose of the API</a></li>
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<li><a href="#unique-data-sources" id="toc-unique-data-sources">Unique Data Sources</a></li>
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<li><a href="#tracking-observations-and-revisions" id="toc-tracking-observations-and-revisions">Tracking Observations and Revisions</a></li>
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<li><a href="#accessing-the-api" id="toc-accessing-the-api">Accessing the API</a></li>
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<li><a href="#putting-the-api-to-work" id="toc-putting-the-api-to-work">Putting the API to Work</a></li>
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<li><a href="#purpose-of-the-api">Purpose of the API</a></li>
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<li><a href="#unique-data-sources">Unique Data Sources</a></li>
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<li><a href="#tracking-observations-and-revisions">Tracking Observations and Revisions</a></li>
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<li><a href="#accessing-the-api">Accessing the API</a></li>
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<li><a href="#putting-the-api-to-work">Putting the API to Work</a></li>
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</ul>
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</div>
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knitr::kable(&quot;html&quot;, digits = 2,
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col.names = c(&quot;Test date&quot;, &quot;Positivity rate (%)&quot;, &quot;Sample size&quot;,
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&quot;Issued on&quot;, &quot;Lag (days)&quot;))</code></pre>
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<p><em>Nov 6 2023 update: Quidel covidtest data is no longer available for public viewing, so we have removed the result of this code chunk.</em></p>
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<table>
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<thead>
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<tr>
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<th style="text-align:left;">
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Test date
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</th>
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<th style="text-align:right;">
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Positivity rate (%)
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</th>
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<th style="text-align:right;">
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Sample size
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</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>
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<tbody>
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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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1.01
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</td>
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<td style="text-align:right;">
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198
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</td>
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<td style="text-align:left;">
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2020-08-06
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</td>
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<td style="text-align:right;">
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5
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</td>
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</tr>
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<tr>
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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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0.97
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</td>
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<td style="text-align:right;">
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206
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</td>
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2020-08-07
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</td>
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6
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</tr>
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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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1.41
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</td>
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<td style="text-align:right;">
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284
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</td>
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<td style="text-align:left;">
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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>
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</tr>
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<tr>
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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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1.38
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</td>
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<td style="text-align:right;">
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290
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</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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11
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</td>
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</tr>
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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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2020-08-16
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</td>
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15
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</td>
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</tr>
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<tr>
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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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1.53
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</td>
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<td style="text-align:right;">
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459
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</td>
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<td style="text-align:left;">
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2020-08-19
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</td>
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<td style="text-align:right;">
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18
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</td>
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</tr>
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<tr>
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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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1.47
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</td>
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<td style="text-align:right;">
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477
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</td>
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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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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
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</td>
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2020-08-01
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<td style="text-align:right;">
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1.36
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</td>
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<td style="text-align:right;">
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513
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</td>
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2020-08-30
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</td>
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<td style="text-align:right;">
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29
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</td>
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</tr>
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</tbody>
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</table>
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<p>Many data sources are subject to revisions:</p>
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<ul>
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<li>Case and death counts are frequently corrected or adjusted by authorities.</li>

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