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@ -186,8 +186,7 @@
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='co'># ----------- #</span>
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<pre class="examples"><div class='input'><span class='co'># ----------- #</span>
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<span class='co'># PREPARATION #</span>
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<span class='co'># ----------- #</span>
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@ -199,8 +198,7 @@
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<span class='co'># Add first isolates to our data set:</span>
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<span class='no'>my_data</span> <span class='kw'><-</span> <span class='no'>my_data</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolates</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>my_data</span>, <span class='st'>"date"</span>, <span class='st'>"patient_id"</span>, <span class='st'>"mo"</span>))
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolates</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>my_data</span>, <span class='st'>"date"</span>, <span class='st'>"patient_id"</span>, <span class='st'>"mo"</span>))</div><div class='output co'>#> <span class='message'>=> Found <span style='font-weight: bold;'>1,317 first isolates</span><span> (65.9% of total)</span></div><div class='input'>
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<span class='co'># -------- #</span>
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<span class='co'># ANALYSIS #</span>
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<span class='co'># -------- #</span>
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@ -213,8 +211,13 @@
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<span class='no'>first_isolates</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>amox</span>),
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<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amox</span>))
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<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amox</span>))</div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 19 results available (minimum set to 30).</span></div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 4 x 3</span><span>
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#> hospital_id n p
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#> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span>
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#> </span><span style='color: #BCBCBC;'>1</span><span> A 19 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>2</span><span> B 65 0.477
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#> </span><span style='color: #BCBCBC;'>3</span><span> C 35 0.543
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#> </span><span style='color: #BCBCBC;'>4</span><span> D 94 0.5 </div><div class='input'>
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<span class='co'># 2. Get the amoxicillin/clavulanic acid resistance</span>
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<span class='co'># percentages of E. coli, trend over the years:</span>
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@ -224,8 +227,25 @@
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<span class='no'>first_isolates</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>amcl</span>),
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<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amcl</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>20</span>))
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<span class='co'># }</span></pre>
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<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amcl</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>20</span>))</div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 14 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 15 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 16 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 18 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 10 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 14 results available (minimum set to 20).</span></div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 16 x 3</span><span>
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#> year n p
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#> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span>
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#> </span><span style='color: #BCBCBC;'> 1</span><span> 2002 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 2</span><span> 2003 14 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 3</span><span> 2004 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 4</span><span> 2005 15 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 5</span><span> 2006 16 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 6</span><span> 2007 17 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 7</span><span> 2008 17 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 8</span><span> 2009 18 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 9</span><span> 2010 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>10</span><span> 2011 21 0.095</span><span style='text-decoration: underline;'>2</span><span>
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#> </span><span style='color: #BCBCBC;'>11</span><span> 2012 10 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>12</span><span> 2013 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>13</span><span> 2014 20 0.2
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#> </span><span style='color: #BCBCBC;'>14</span><span> 2015 14 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>15</span><span> 2016 21 0.190
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#> </span><span style='color: #BCBCBC;'>16</span><span> 2017 20 0.4 </div></span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
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