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updated the website
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@eeholmes
eeholmes committed Mar 25, 2020
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5 changes: 5 additions & 0 deletions CoV19.Rproj
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Expand Up @@ -11,3 +11,8 @@ Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX

BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate
2 changes: 1 addition & 1 deletion _site.yml
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Expand Up @@ -16,7 +16,7 @@ navbar:
- text: "All States"
icon: fa-bullhorn
href: state_plots.html
- text: "Epidemic States"
- text: "Select States"
icon: fa-bullhorn
href: epidemic_states.html
- text: "Lombardy Comparison"
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29 changes: 11 additions & 18 deletions docs/data.html
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<a href="epidemic_states.html">
<span class="fa fa-bullhorn"></span>

Epidemic States
Select States
</a>
</li>
<li>
Expand Down Expand Up @@ -334,35 +334,28 @@ <h1 class="title toc-ignore">Data</h1>


<p>Load the package.</p>
<pre><code>library(CoV19)</code></pre>
<pre class="r"><code>library(CoV19)</code></pre>
<p>The data are in the following objects. They have a few common columns: date, region, positive, death. Then there are some other columns depending on the source.</p>
<pre><code>states
italy
world</code></pre>
<p>Here is an example from <code>states</code>:</p>
<pre class="r"><code>head(states)</code></pre>
<pre><code>## date region positive negative pending hospitalized
## 1 2020-03-24 AK 36 986 NA 0
## 2 2020-03-24 AL 215 2106 NA NA
## 3 2020-03-24 AR 218 947 0 22
## 4 2020-03-24 AS 0 NA NA NA
## 5 2020-03-24 AZ 357 313 22 8
## 6 2020-03-24 CA 1733 12567 12100 NA
## death total.tests
## 1 NA 1022
## 2 0 2321
## 3 0 1165
## 4 0 0
## 5 5 692
## 6 27 26400</code></pre>
<pre><code>## date region positive negative pending hospitalized death total.tests
## 1 2020-03-24 AK 36 986 NA 0 NA 1022
## 2 2020-03-24 AL 215 2106 NA NA 0 2321
## 3 2020-03-24 AR 218 947 0 22 0 1165
## 4 2020-03-24 AS 0 NA NA NA 0 0
## 5 2020-03-24 AZ 357 313 22 8 5 692
## 6 2020-03-24 CA 1733 12567 12100 NA 27 26400</code></pre>
<div id="subsetting-data" class="section level1">
<h1>Subsetting data</h1>
<pre class="r"><code># Just WA
x &lt;- subset(states, region==&quot;WA&quot;)
# Two states
x &lt;- subset(states, region %in% c(&quot;WA&quot;,&quot;CA&quot;))
# All areas in China
x &lt;- subset(world, str_detect(region, &quot;China&quot;))</code></pre>
x &lt;- subset(world, stringr::str_detect(region, &quot;China&quot;))</code></pre>
</div>
<div id="merging-data" class="section level1">
<h1>Merging Data</h1>
Expand All @@ -378,7 +371,7 @@ <h1>Merging Data</h1>
x$region &lt;- as.factor(&quot;WA + CA + OR&quot;)</code></pre>
<p>We can pass this data object to <code>plot2</code> to plot.</p>
<pre class="r"><code>plot2(x)</code></pre>
<p><img src="data_files/figure-html/unnamed-chunk-4-1.png" width="672" /></p>
<p><img src="data_files/figure-html/unnamed-chunk-9-1.png" width="672" /></p>
</div>


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8 changes: 3 additions & 5 deletions docs/epidemic_states.html
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Expand Up @@ -306,7 +306,7 @@
<a href="epidemic_states.html">
<span class="fa fa-bullhorn"></span>

Epidemic States
Select States
</a>
</li>
<li>
Expand Down Expand Up @@ -336,11 +336,9 @@ <h1 class="title toc-ignore">Epidemic State Plots</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;NY&quot;, &quot;NJ&quot;))</code></pre>
<p><img src="epidemic_states_files/figure-html/unnamed-chunk-1-1.png" width="672" /></p>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;WA&quot;, &quot;CA&quot;))</code></pre>
<pre class="r"><code>plot2(states, c(&quot;WA&quot;, &quot;CA&quot;))</code></pre>
<p><img src="epidemic_states_files/figure-html/unnamed-chunk-2-1.png" width="672" /></p>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;FL&quot;, &quot;CO&quot;))</code></pre>
<pre class="r"><code>plot2(states, c(&quot;FL&quot;, &quot;CO&quot;))</code></pre>
<p><img src="epidemic_states_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>


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2 changes: 1 addition & 1 deletion docs/index.html
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Expand Up @@ -306,7 +306,7 @@
<a href="epidemic_states.html">
<span class="fa fa-bullhorn"></span>

Epidemic States
Select States
</a>
</li>
<li>
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2 changes: 1 addition & 1 deletion docs/plots.html
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Expand Up @@ -306,7 +306,7 @@
<a href="epidemic_states.html">
<span class="fa fa-bullhorn"></span>

Epidemic States
Select States
</a>
</li>
<li>
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50 changes: 20 additions & 30 deletions docs/state_plots.html
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Expand Up @@ -306,7 +306,7 @@
<a href="epidemic_states.html">
<span class="fa fa-bullhorn"></span>

Epidemic States
Select States
</a>
</li>
<li>
Expand All @@ -333,59 +333,49 @@ <h1 class="title toc-ignore">State Plots</h1>
</div>


<pre class="r"><code>library(CoV19)</code></pre>
<div id="south" class="section level1">
<h1>South</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;FL&quot;,&quot;LA&quot;,&quot;GA&quot;,&quot;MS&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-1-1.png" width="672" /></p>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;SC&quot;,&quot;NC&quot;,&quot;VA&quot;,&quot;WV&quot;))</code></pre>
<pre class="r"><code>plot2(states, c(&quot;FL&quot;,&quot;LA&quot;,&quot;GA&quot;,&quot;MS&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-2-1.png" width="672" /></p>
<pre class="r"><code>plot2(states, c(&quot;SC&quot;,&quot;NC&quot;,&quot;VA&quot;,&quot;WV&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
</div>
<div id="northeast" class="section level1">
<h1>Northeast</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;NY&quot;,&quot;NJ&quot;,&quot;PA&quot;,&quot;CT&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;VT&quot;,&quot;ME&quot;,&quot;NH&quot;,&quot;MA&quot;))</code></pre>
<pre class="r"><code>plot2(states, c(&quot;NY&quot;,&quot;NJ&quot;,&quot;PA&quot;,&quot;CT&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-4-1.png" width="672" /></p>
<pre class="r"><code>plot2(states, c(&quot;VT&quot;,&quot;ME&quot;,&quot;NH&quot;,&quot;MA&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-5-1.png" width="672" /></p>
</div>
<div id="midwest" class="section level1">
<h1>Midwest</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;OH&quot;,&quot;IN&quot;,&quot;IL&quot;,&quot;MI&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-5-1.png" width="672" /></p>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;WI&quot;,&quot;MN&quot;,&quot;IA&quot;,&quot;MO&quot;))</code></pre>
<pre class="r"><code>plot2(states, c(&quot;OH&quot;,&quot;IN&quot;,&quot;IL&quot;,&quot;MI&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-6-1.png" width="672" /></p>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;ND&quot;,&quot;SD&quot;,&quot;NE&quot;,&quot;KS&quot;))</code></pre>
<pre class="r"><code>plot2(states, c(&quot;WI&quot;,&quot;MN&quot;,&quot;IA&quot;,&quot;MO&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-7-1.png" width="672" /></p>
<pre class="r"><code>plot2(states, c(&quot;ND&quot;,&quot;SD&quot;,&quot;NE&quot;,&quot;KS&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-8-1.png" width="672" /></p>
</div>
<div id="north-rockies" class="section level1">
<h1>North Rockies</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;ID&quot;,&quot;WY&quot;,&quot;MT&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-8-1.png" width="672" /></p>
<pre class="r"><code>plot2(states, c(&quot;ID&quot;,&quot;WY&quot;,&quot;MT&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-9-1.png" width="672" /></p>
</div>
<div id="four-corners" class="section level1">
<h1>Four Corners</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;AZ&quot;,&quot;UT&quot;,&quot;CO&quot;,&quot;NM&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-9-1.png" width="672" /></p>
<pre class="r"><code>plot2(states, c(&quot;AZ&quot;,&quot;UT&quot;,&quot;CO&quot;,&quot;NM&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-10-1.png" width="672" /></p>
</div>
<div id="texas-and-company" class="section level1">
<h1>Texas and company</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;TX&quot;,&quot;OK&quot;,&quot;AR&quot;,&quot;LA&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-10-1.png" width="672" /></p>
<pre class="r"><code>plot2(states, c(&quot;TX&quot;,&quot;OK&quot;,&quot;AR&quot;,&quot;LA&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-11-1.png" width="672" /></p>
</div>
<div id="west" class="section level1">
<h1>West</h1>
<pre class="r"><code>library(CoV19)
plot2(states, c(&quot;CA&quot;,&quot;OR&quot;,&quot;WA&quot;,&quot;NV&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-11-1.png" width="672" /></p>
<pre class="r"><code>plot2(states, c(&quot;CA&quot;,&quot;OR&quot;,&quot;WA&quot;,&quot;NV&quot;))</code></pre>
<p><img src="state_plots_files/figure-html/unnamed-chunk-12-1.png" width="672" /></p>
</div>


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16 changes: 11 additions & 5 deletions docs/walomb_plot.html
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Expand Up @@ -306,7 +306,7 @@
<a href="epidemic_states.html">
<span class="fa fa-bullhorn"></span>

Epidemic States
Select States
</a>
</li>
<li>
Expand All @@ -333,11 +333,17 @@ <h1 class="title toc-ignore">Lombardy vs WA Plots</h1>
</div>


<pre class="r"><code>library(CoV19)
my_plot(italy, &quot;Lombardia&quot;, &quot;2020-03-10&quot;)</code></pre>
<p><img src="walomb_plot_files/figure-html/unnamed-chunk-1-1.png" width="672" /></p>
<pre class="r"><code>my_plot(states, &quot;WA&quot;, &quot;2020-03-16&quot;)</code></pre>
<pre class="r"><code>library(CoV19)</code></pre>
<pre class="r"><code>my_plot(italy, &quot;Lombardia&quot;, &quot;2020-03-10&quot;)</code></pre>
<p><img src="walomb_plot_files/figure-html/unnamed-chunk-2-1.png" width="672" /></p>
<pre class="r"><code>x &lt;- subset(states, region==&quot;WA&quot;)
x &lt;- rbind(x, data.frame(date=as.Date(&quot;2020-03-25&quot;), region=&quot;WA&quot;, positive=2469, negative=NA, pending=NA, hospitalized=NA, death=123, total.tests=NA))
my_plot(x, &quot;WA&quot;, &quot;2020-03-16&quot;)</code></pre>
<p><img src="walomb_plot_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
<pre class="r"><code>x &lt;- world
x[x$date==&quot;2020-02-12&quot;,&quot;positive&quot;]=NA
x[x$date==&quot;2020-02-13&quot;,&quot;positive&quot;]=NA
p &lt;- my_plot(x, &quot;Hubei China&quot;, &quot;2020-01-23&quot;)</code></pre>



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