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@@ -36,7 +36,7 @@
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+1
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+249
-251
@@ -38,7 +38,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -317,69 +317,69 @@
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</tr></thead>
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<tbody>
|
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<tr class="odd">
|
||||
<td align="center">2014-01-13</td>
|
||||
<td align="center">A7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">2011-06-19</td>
|
||||
<td align="center">N8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-07-08</td>
|
||||
<td align="center">U10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-07-14</td>
|
||||
<td align="center">N3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-07-17</td>
|
||||
<td align="center">K10</td>
|
||||
<td align="center">2014-07-29</td>
|
||||
<td align="center">J1</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2013-12-06</td>
|
||||
<td align="center">Z6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-09-04</td>
|
||||
<td align="center">U4</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-05-09</td>
|
||||
<td align="center">B3</td>
|
||||
<td align="center">2015-03-05</td>
|
||||
<td align="center">A9</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-10-20</td>
|
||||
<td align="center">P10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-12-21</td>
|
||||
<td align="center">U3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@@ -414,16 +414,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,403</td>
|
||||
<td align="right">52.02%</td>
|
||||
<td align="right">10,403</td>
|
||||
<td align="right">52.02%</td>
|
||||
<td align="right">10,328</td>
|
||||
<td align="right">51.64%</td>
|
||||
<td align="right">10,328</td>
|
||||
<td align="right">51.64%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,597</td>
|
||||
<td align="right">47.99%</td>
|
||||
<td align="right">9,672</td>
|
||||
<td align="right">48.36%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@@ -477,9 +477,9 @@ Longest: 1</p>
|
||||
<span><span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span></span>
|
||||
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
|
||||
<span><span class="co"># 2</span></span>
|
||||
<span><span class="co"># => Found 10,723 'phenotype-based' first isolates (53.6% of total where a</span></span>
|
||||
<span><span class="co"># => Found 10,619 'phenotype-based' first isolates (53.1% of total where a</span></span>
|
||||
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
|
||||
<p>So only 53.6% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<p>So only 53.1% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||||
@@ -487,7 +487,7 @@ Longest: 1</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>So we end up with 10,723 isolates for analysis. Now our data looks like:</p>
|
||||
<p>So we end up with 10,619 isolates for analysis. Now our data looks like:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
|
||||
<table style="width:100%;" class="table">
|
||||
@@ -525,101 +525,101 @@ Longest: 1</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="center">2014-01-13</td>
|
||||
<td align="center">A7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">3</td>
|
||||
<td align="center">2013-12-06</td>
|
||||
<td align="center">Z6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="center">2010-05-09</td>
|
||||
<td align="center">B3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">2015-03-05</td>
|
||||
<td align="center">A9</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">6</td>
|
||||
<td align="center">2013-12-21</td>
|
||||
<td align="center">U3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">2017-10-20</td>
|
||||
<td align="center">P10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">8</td>
|
||||
<td align="center">2013-03-11</td>
|
||||
<td align="center">S7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">7</td>
|
||||
<td align="center">2011-06-10</td>
|
||||
<td align="center">D8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">9</td>
|
||||
<td align="center">2012-03-02</td>
|
||||
<td align="center">K7</td>
|
||||
<td align="center">2012-06-14</td>
|
||||
<td align="center">I1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">10</td>
|
||||
<td align="center">2010-11-23</td>
|
||||
<td align="center">V10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">13</td>
|
||||
<td align="center">2012-03-06</td>
|
||||
<td align="center">R5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Time for the analysis!</p>
|
||||
@@ -641,8 +641,8 @@ Longest: 1</p>
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 10,723<br>
|
||||
Available: 10,723 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Length: 10,619<br>
|
||||
Available: 10,619 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@@ -659,33 +659,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">4,683</td>
|
||||
<td align="right">43.67%</td>
|
||||
<td align="right">4,683</td>
|
||||
<td align="right">43.67%</td>
|
||||
<td align="right">4,632</td>
|
||||
<td align="right">43.62%</td>
|
||||
<td align="right">4,632</td>
|
||||
<td align="right">43.62%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">2,727</td>
|
||||
<td align="right">25.43%</td>
|
||||
<td align="right">7,410</td>
|
||||
<td align="right">69.10%</td>
|
||||
<td align="right">2,742</td>
|
||||
<td align="right">25.82%</td>
|
||||
<td align="right">7,374</td>
|
||||
<td align="right">69.44%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,104</td>
|
||||
<td align="right">19.62%</td>
|
||||
<td align="right">9,514</td>
|
||||
<td align="right">88.73%</td>
|
||||
<td align="right">2,062</td>
|
||||
<td align="right">19.42%</td>
|
||||
<td align="right">9,436</td>
|
||||
<td align="right">88.86%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,209</td>
|
||||
<td align="right">11.27%</td>
|
||||
<td align="right">10,723</td>
|
||||
<td align="right">1,183</td>
|
||||
<td align="right">11.14%</td>
|
||||
<td align="right">10,619</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@@ -704,14 +704,14 @@ Longest: 24</p>
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="11%">
|
||||
<col width="10%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@@ -732,13 +732,13 @@ Longest: 24</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2013-12-06</td>
|
||||
<td align="center">Z6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2010-11-23</td>
|
||||
<td align="center">V10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
@@ -747,23 +747,8 @@ Longest: 24</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-12-21</td>
|
||||
<td align="center">U3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-06-10</td>
|
||||
<td align="center">D8</td>
|
||||
<td align="center">2011-11-01</td>
|
||||
<td align="center">B1</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
@@ -776,9 +761,24 @@ Longest: 24</p>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-01-30</td>
|
||||
<td align="center">H5</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-03-02</td>
|
||||
<td align="center">K7</td>
|
||||
<td align="center">2015-12-11</td>
|
||||
<td align="center">I5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
@@ -792,9 +792,24 @@ Longest: 24</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-12-25</td>
|
||||
<td align="center">W10</td>
|
||||
<td align="center">2017-08-04</td>
|
||||
<td align="center">O3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-10-06</td>
|
||||
<td align="center">V8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -806,21 +821,6 @@ Longest: 24</p>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-02-13</td>
|
||||
<td align="center">E5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
|
||||
@@ -842,50 +842,50 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">2228</td>
|
||||
<td align="center">121</td>
|
||||
<td align="center">2334</td>
|
||||
<td align="center">4683</td>
|
||||
<td align="center">2203</td>
|
||||
<td align="center">123</td>
|
||||
<td align="center">2306</td>
|
||||
<td align="center">4632</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">3423</td>
|
||||
<td align="center">156</td>
|
||||
<td align="center">1104</td>
|
||||
<td align="center">4683</td>
|
||||
<td align="center">3385</td>
|
||||
<td align="center">145</td>
|
||||
<td align="center">1102</td>
|
||||
<td align="center">4632</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3439</td>
|
||||
<td align="center">3390</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1244</td>
|
||||
<td align="center">4683</td>
|
||||
<td align="center">1242</td>
|
||||
<td align="center">4632</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4064</td>
|
||||
<td align="center">4049</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">619</td>
|
||||
<td align="center">4683</td>
|
||||
<td align="center">583</td>
|
||||
<td align="center">4632</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1209</td>
|
||||
<td align="center">1209</td>
|
||||
<td align="center">1183</td>
|
||||
<td align="center">1183</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">960</td>
|
||||
<td align="center">46</td>
|
||||
<td align="center">203</td>
|
||||
<td align="center">1209</td>
|
||||
<td align="center">929</td>
|
||||
<td align="center">54</td>
|
||||
<td align="center">200</td>
|
||||
<td align="center">1183</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -908,34 +908,34 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4064</td>
|
||||
<td align="center">4049</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">619</td>
|
||||
<td align="center">4683</td>
|
||||
<td align="center">583</td>
|
||||
<td align="center">4632</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">1075</td>
|
||||
<td align="center">1078</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">134</td>
|
||||
<td align="center">1209</td>
|
||||
<td align="center">105</td>
|
||||
<td align="center">1183</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">2421</td>
|
||||
<td align="center">2430</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">306</td>
|
||||
<td align="center">2727</td>
|
||||
<td align="center">312</td>
|
||||
<td align="center">2742</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">S. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">2104</td>
|
||||
<td align="center">2104</td>
|
||||
<td align="center">2062</td>
|
||||
<td align="center">2062</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -949,7 +949,7 @@ Longest: 24</p>
|
||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
||||
<span><span class="co"># [1] 0.5465821</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 0.5432715</span></span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
@@ -963,19 +963,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5332098</td>
|
||||
<td align="center">0.5382868</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5497618</td>
|
||||
<td align="center">0.5447543</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5499058</td>
|
||||
<td align="center">0.5595602</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5588652</td>
|
||||
<td align="center">0.5353630</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -994,23 +994,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5332098</td>
|
||||
<td align="center">3237</td>
|
||||
<td align="center">0.5382868</td>
|
||||
<td align="center">3082</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5497618</td>
|
||||
<td align="center">3778</td>
|
||||
<td align="center">0.5447543</td>
|
||||
<td align="center">3765</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5499058</td>
|
||||
<td align="center">1593</td>
|
||||
<td align="center">0.5595602</td>
|
||||
<td align="center">1637</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5588652</td>
|
||||
<td align="center">2115</td>
|
||||
<td align="center">0.5353630</td>
|
||||
<td align="center">2135</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1031,27 +1031,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7642537</td>
|
||||
<td align="center">0.8678198</td>
|
||||
<td align="center">0.9750160</td>
|
||||
<td align="center">0.7620898</td>
|
||||
<td align="center">0.8741364</td>
|
||||
<td align="center">0.9771157</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8320926</td>
|
||||
<td align="center">0.8891646</td>
|
||||
<td align="center">0.9743590</td>
|
||||
<td align="center">0.8309383</td>
|
||||
<td align="center">0.9112426</td>
|
||||
<td align="center">0.9805579</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7920792</td>
|
||||
<td align="center">0.8877888</td>
|
||||
<td align="center">0.9845985</td>
|
||||
<td align="center">0.7884756</td>
|
||||
<td align="center">0.8862144</td>
|
||||
<td align="center">0.9817651</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5361217</td>
|
||||
<td align="center">0.5354025</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5361217</td>
|
||||
<td align="center">0.5354025</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1076,23 +1076,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital A</td>
|
||||
<td align="right">53.3%</td>
|
||||
<td align="right">53.8%</td>
|
||||
<td align="right">26.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital B</td>
|
||||
<td align="right">55.0%</td>
|
||||
<td align="right">54.5%</td>
|
||||
<td align="right">27.0%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital C</td>
|
||||
<td align="right">55.0%</td>
|
||||
<td align="right">25.5%</td>
|
||||
<td align="right">56.0%</td>
|
||||
<td align="right">27.9%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital D</td>
|
||||
<td align="right">55.9%</td>
|
||||
<td align="right">27.3%</td>
|
||||
<td align="right">53.5%</td>
|
||||
<td align="right">26.1%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1176,18 +1176,16 @@ Longest: 24</p>
|
||||
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
|
||||
<span><span class="va">mic_values</span></span>
|
||||
<span><span class="co"># Class <mic></span></span>
|
||||
<span><span class="co"># [1] 32 64 128 128 64 8 32 0.002 0.025 </span></span>
|
||||
<span><span class="co"># [10] 0.5 32 <=0.001 2 128 0.01 1 2 0.01 </span></span>
|
||||
<span><span class="co"># [19] 128 0.5 4 0.002 0.125 256 0.0625 4 0.002 </span></span>
|
||||
<span><span class="co"># [28] 0.005 4 0.002 32 0.01 0.0625 0.25 2 64 </span></span>
|
||||
<span><span class="co"># [37] 0.0625 0.5 256 4 1 0.025 128 0.0625 16 </span></span>
|
||||
<span><span class="co"># [46] 0.5 0.005 0.01 1 2 0.01 2 8 0.125 </span></span>
|
||||
<span><span class="co"># [55] 0.25 256 0.0625 0.025 0.002 8 <=0.001 1 0.002 </span></span>
|
||||
<span><span class="co"># [64] 256 8 4 0.005 0.025 4 0.002 <=0.001 2 </span></span>
|
||||
<span><span class="co"># [73] 256 0.005 256 2 4 16 128 256 <=0.001</span></span>
|
||||
<span><span class="co"># [82] 1 2 1 1 <=0.001 0.5 4 0.25 32 </span></span>
|
||||
<span><span class="co"># [91] 0.002 0.0625 0.01 32 0.005 0.01 2 64 64 </span></span>
|
||||
<span><span class="co"># [100] 2</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 256 16 0.002 0.025 8 0.025 32 0.025 0.01 256 </span></span>
|
||||
<span><span class="co"># [11] 16 0.01 32 0.025 0.01 0.0625 2 0.25 128 0.005 </span></span>
|
||||
<span><span class="co"># [21] 0.01 16 0.125 0.25 0.01 0.001 8 0.025 8 1 </span></span>
|
||||
<span><span class="co"># [31] 0.025 0.25 0.0625 256 0.001 0.025 0.001 8 0.01 0.025 </span></span>
|
||||
<span><span class="co"># [41] 0.25 8 64 8 0.25 4 1 0.0625 0.0625 0.5 </span></span>
|
||||
<span><span class="co"># [51] 2 0.002 16 0.002 0.01 16 0.25 64 8 256 </span></span>
|
||||
<span><span class="co"># [61] 0.005 0.0625 1 64 64 0.5 128 0.002 32 0.002 </span></span>
|
||||
<span><span class="co"># [71] 128 128 0.5 0.002 0.25 0.5 0.125 1 16 64 </span></span>
|
||||
<span><span class="co"># [81] 128 32 0.025 128 16 32 32 32 0.002 0.125 </span></span>
|
||||
<span><span class="co"># [91] 0.5 0.0625 0.5 128 0.125 128 8 0.25 128 0.25</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
|
||||
@@ -1216,10 +1214,10 @@ Longest: 24</p>
|
||||
<span><span class="co"># coli). Run `mo_uncertainties()` to review this.</span></span>
|
||||
<span><span class="va">disk_values</span></span>
|
||||
<span><span class="co"># Class <disk></span></span>
|
||||
<span><span class="co"># [1] 28 22 30 19 23 20 17 21 22 18 18 27 18 20 24 28 30 20 29 31 22 31 23 24 17</span></span>
|
||||
<span><span class="co"># [26] 23 18 17 25 30 28 23 30 23 30 31 18 26 26 26 27 17 30 18 27 31 17 24 20 26</span></span>
|
||||
<span><span class="co"># [51] 30 21 26 27 20 23 28 29 17 29 27 24 22 27 28 27 22 30 18 28 25 18 25 18 31</span></span>
|
||||
<span><span class="co"># [76] 29 25 17 31 20 20 21 24 24 30 28 30 31 20 30 27 19 24 17 22 30 31 27 28 24</span></span></code></pre></div>
|
||||
<span><span class="co"># [1] 23 21 25 21 18 21 18 19 23 26 28 30 20 21 17 17 27 26 31 30 25 17 27 27 19</span></span>
|
||||
<span><span class="co"># [26] 31 23 23 23 22 20 26 17 24 29 26 24 25 29 22 22 29 26 22 24 25 26 18 31 24</span></span>
|
||||
<span><span class="co"># [51] 25 28 26 27 19 21 21 29 27 21 27 21 18 17 20 20 17 25 30 20 19 20 23 27 31</span></span>
|
||||
<span><span class="co"># [76] 24 31 24 22 26 19 19 20 20 25 17 21 22 30 25 23 26 31 20 30 18 29 18 29 17</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
|
||||
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
|
||||
|
||||
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@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+29
-29
@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -313,18 +313,18 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co"># 1 I I S S I R</span></span>
|
||||
<span><span class="co"># 2 I R R S I I</span></span>
|
||||
<span><span class="co"># 3 R I S R R S</span></span>
|
||||
<span><span class="co"># 4 I S I S I S</span></span>
|
||||
<span><span class="co"># 5 S R S I S R</span></span>
|
||||
<span><span class="co"># 6 I S I I S S</span></span>
|
||||
<span><span class="co"># 1 S S R I R I</span></span>
|
||||
<span><span class="co"># 2 I R S S S S</span></span>
|
||||
<span><span class="co"># 3 I R S I S S</span></span>
|
||||
<span><span class="co"># 4 R I S I S R</span></span>
|
||||
<span><span class="co"># 5 I I S R S R</span></span>
|
||||
<span><span class="co"># 6 S I S S R R</span></span>
|
||||
<span><span class="co"># kanamycin</span></span>
|
||||
<span><span class="co"># 1 I</span></span>
|
||||
<span><span class="co"># 2 R</span></span>
|
||||
<span><span class="co"># 3 S</span></span>
|
||||
<span><span class="co"># 1 S</span></span>
|
||||
<span><span class="co"># 2 S</span></span>
|
||||
<span><span class="co"># 3 I</span></span>
|
||||
<span><span class="co"># 4 R</span></span>
|
||||
<span><span class="co"># 5 S</span></span>
|
||||
<span><span class="co"># 5 I</span></span>
|
||||
<span><span class="co"># 6 S</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
@@ -356,40 +356,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3193</td>
|
||||
<td align="right">63.86%</td>
|
||||
<td align="right">3193</td>
|
||||
<td align="right">63.86%</td>
|
||||
<td align="right">3182</td>
|
||||
<td align="right">63.64%</td>
|
||||
<td align="right">3182</td>
|
||||
<td align="right">63.64%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">996</td>
|
||||
<td align="right">19.92%</td>
|
||||
<td align="right">4189</td>
|
||||
<td align="right">83.78%</td>
|
||||
<td align="right">993</td>
|
||||
<td align="right">19.86%</td>
|
||||
<td align="right">4175</td>
|
||||
<td align="right">83.50%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">450</td>
|
||||
<td align="right">9.00%</td>
|
||||
<td align="right">4639</td>
|
||||
<td align="right">92.78%</td>
|
||||
<td align="right">477</td>
|
||||
<td align="right">9.54%</td>
|
||||
<td align="right">4652</td>
|
||||
<td align="right">93.04%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">241</td>
|
||||
<td align="right">4.82%</td>
|
||||
<td align="right">4880</td>
|
||||
<td align="right">97.60%</td>
|
||||
<td align="right">250</td>
|
||||
<td align="right">5.00%</td>
|
||||
<td align="right">4902</td>
|
||||
<td align="right">98.04%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">120</td>
|
||||
<td align="right">2.40%</td>
|
||||
<td align="right">98</td>
|
||||
<td align="right">1.96%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
||||
+1
-1
@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+1
-1
@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -184,7 +184,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</h2>
|
||||
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
|
||||
@@ -405,7 +405,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
|
||||
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
|
||||
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
|
||||
@@ -470,7 +470,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</h2>
|
||||
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
||||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
|
||||
@@ -638,7 +638,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</h2>
|
||||
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
|
||||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
|
||||
@@ -765,7 +765,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</h2>
|
||||
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (49 kB)<br>
|
||||
@@ -919,7 +919,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</h2>
|
||||
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
|
||||
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
|
||||
@@ -1186,7 +1186,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</h2>
|
||||
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
|
||||
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 21 August 2022 14:52:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
|
||||
|
||||
+1
-1
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -176,7 +176,7 @@
|
||||
<div class="section level2">
|
||||
<h2 id="needed-r-packages">Needed R packages<a class="anchor" aria-label="anchor" href="#needed-r-packages"></a>
|
||||
</h2>
|
||||
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
|
||||
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a>. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
|
||||
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
|
||||
@@ -205,9 +205,8 @@
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
|
||||
<pre><code><span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre>
|
||||
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">predict_TZP</span></span>
|
||||
<span><span class="co"># year value se_min se_max observations observed estimated</span></span>
|
||||
<span><span class="co"># 1 2002 0.20000000 NA NA 15 0.20000000 0.05616378</span></span>
|
||||
@@ -242,15 +241,15 @@
|
||||
<span><span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span></span>
|
||||
<span><span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></span></code></pre></div>
|
||||
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
|
||||
<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
|
||||
<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span></span>
|
||||
<span><span class="co"># choose for error bars instead of a ribbon</span></span>
|
||||
<span><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span>, ribbon <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
|
||||
@@ -259,7 +258,7 @@
|
||||
<h3 id="choosing-the-right-model">Choosing the right model<a class="anchor" aria-label="anchor" href="#choosing-the-right-model"></a>
|
||||
</h3>
|
||||
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
@@ -305,7 +304,7 @@
|
||||
</tbody>
|
||||
</table>
|
||||
<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
@@ -313,7 +312,7 @@
|
||||
<span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span></span>
|
||||
|
||||
@@ -38,7 +38,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+1
-1
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+1
-1
@@ -1 +1 @@
|
||||
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||||
@import url("font.css");:root{--bs-blue: #2c3e50;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #e83e8c;--bs-red: #e74c3c;--bs-orange: #fd7e14;--bs-yellow: #f39c12;--bs-green: #18bc9c;--bs-teal: #20c997;--bs-cyan: #3498db;--bs-white: #fff;--bs-gray: #95a5a6;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #ecf0f1;--bs-gray-300: #dee2e6;--bs-gray-400: #ced4da;--bs-gray-500: #b4bcc2;--bs-gray-600: #95a5a6;--bs-gray-700: #7b8a8b;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #95a5a6;--bs-primary: #2c3e50;--bs-secondary: #95a5a6;--bs-success: #128F76;--bs-info: #3498db;--bs-warning: #f39c12;--bs-danger: #e74c3c;--bs-light: #ecf0f1;--bs-dark: #7b8a8b;--bs-default-rgb: 149,165,166;--bs-primary-rgb: 44,62,80;--bs-secondary-rgb: 149,165,166;--bs-success-rgb: 18,143,118;--bs-info-rgb: 52,152,219;--bs-warning-rgb: 243,156,18;--bs-danger-rgb: 231,76,60;--bs-light-rgb: 236,240,241;--bs-dark-rgb: 123,138,139;--bs-white-rgb: 255,255,255;--bs-black-rgb: 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no-preference){:root{scroll-behavior:smooth}}body{margin:0;font-family:var(--bs-body-font-family);font-size:var(--bs-body-font-size);font-weight:var(--bs-body-font-weight);line-height:var(--bs-body-line-height);color:var(--bs-body-color);text-align:var(--bs-body-text-align);background-color:var(--bs-body-bg);-webkit-text-size-adjust:100%;-webkit-tap-highlight-color:rgba(0,0,0,0)}hr{margin:1rem 0;color:inherit;background-color:currentColor;border:0;opacity:.25}hr:not([size]){height:1px}h6,.h6,h5,.h5,h4,.h4,h3,.h3,h2,.h2,h1,.h1{margin-top:0;margin-bottom:.5rem;font-weight:500;line-height:1.2}h1,.h1{font-size:calc(1.425rem + 2.1vw)}@media (min-width: 1200px){h1,.h1{font-size:3rem}}h2,.h2{font-size:calc(1.375rem + 1.5vw)}@media (min-width: 1200px){h2,.h2{font-size:2.5rem}}h3,.h3{font-size:calc(1.325rem + .9vw)}@media (min-width: 1200px){h3,.h3{font-size:2rem}}h4,.h4{font-size:calc(1.275rem + .3vw)}@media (min-width: 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code{background-color:transparent;font-size:inherit;color:inherit;word-break:normal}code{font-size:.875em;color:#000;background-color:#f6f6f6;border-radius:.25rem;padding:.125rem .25rem;word-wrap:break-word}a>code{color:inherit}kbd{padding:.2rem .4rem;font-size:.875em;color:#fff;background-color:#212529;border-radius:.2rem}kbd kbd{padding:0;font-size:1em;font-weight:700}figure{margin:0 0 1rem}img,svg{vertical-align:middle}table{caption-side:bottom;border-collapse:collapse}caption{padding-top:.5rem;padding-bottom:.5rem;color:#95a5a6;text-align:left}th{text-align:inherit;text-align:-webkit-match-parent}thead,tbody,tfoot,tr,td,th{border-color:inherit;border-style:solid;border-width:0}label{display:inline-block}button{border-radius:0}button:focus:not(:focus-visible){outline:0}input,button,select,optgroup,textarea{margin:0;font-family:inherit;font-siLine truncated
|
||||
@@ -28,15 +28,16 @@
|
||||
$(document).ready(function() {
|
||||
|
||||
// replace \donttest and \dontrun texts in Examples
|
||||
if ($(".ref-examples pre").length > 0) {
|
||||
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\donttest{", ""));
|
||||
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\dontrun{", ""));
|
||||
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# }", ""));
|
||||
if ($("#ref-examples ~ div pre").length > 0) {
|
||||
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", ""));
|
||||
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
|
||||
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
|
||||
}
|
||||
|
||||
// remove leading newline in code examples on changelog
|
||||
if ($("body .template-news").length > 0) {
|
||||
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
|
||||
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R"><span></span>\n<span', 'sourceCode R"><span'));
|
||||
}
|
||||
|
||||
// add doctoral titles to authors
|
||||
|
||||
+1
-1
@@ -44,7 +44,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+5
-5
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -132,14 +132,14 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="1.8.1.9020" id="amr-1819020">AMR 1.8.1.9020<a class="anchor" aria-label="anchor" href="#amr-1819020"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="1.8.1.9021" id="amr-1819021">AMR 1.8.1.9021<a class="anchor" aria-label="anchor" href="#amr-1819021"></a></h2>
|
||||
<div class="section level4">
|
||||
<h4 id="new-1-8-1-9020">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9020"></a></h4>
|
||||
<h4 id="new-1-8-1-9021">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9021"></a></h4>
|
||||
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
|
||||
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. The <code>AMR</code> package is now available in 16 languages.</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="changed-1-8-1-9020">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9020"></a></h4>
|
||||
<h4 id="changed-1-8-1-9021">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9021"></a></h4>
|
||||
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
|
||||
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
|
||||
<li>
|
||||
@@ -157,7 +157,7 @@
|
||||
</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="other-1-8-1-9020">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9020"></a></h4>
|
||||
<h4 id="other-1-8-1-9021">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1-9021"></a></h4>
|
||||
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown v2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
|
||||
<li>Added Peter Dutey-Magni and Anton Mymrikov as contributors, to thank them for their valuable input</li>
|
||||
</ul></div>
|
||||
|
||||
+1
-1
@@ -11,7 +11,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2022-08-21T14:56Z
|
||||
last_built: 2022-08-21T15:26Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+1
-1
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 13 KiB After Width: | Height: | Size: 13 KiB |
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|
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|
After Width: | Height: | Size: 8.3 KiB |
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+11
-11
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -195,16 +195,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1947-08-14 75 75.01918 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1934-01-26 88 88.56712 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1961-06-01 61 61.22192 38</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1994-03-19 28 28.42466 5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1992-01-08 30 30.61644 7</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1946-07-13 76 76.10685 53</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1984-02-02 38 38.54795 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1951-09-30 70 70.89041 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1980-03-07 42 42.45753 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1991-06-28 31 31.14795 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1955-03-05 67 67.46301 44</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1969-09-23 52 52.90959 30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1952-10-15 69 69.84932 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1940-09-07 81 81.95342 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1956-10-12 65 65.85753 43</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1997-03-26 25 25.40548 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1946-04-17 76 76.34521 53</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1987-04-28 35 35.31507 12</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1957-09-27 64 64.89863 42</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1949-07-17 73 73.09589 50</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
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||||
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@@ -168,7 +168,7 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Included in this AMR package (v1.8.1.9020) are:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Included in this AMR package (v1.8.1.9021) are:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Catalogue of Life: 2019 Annual Checklist</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Available at: http://www.catalogueoflife.org</span>
|
||||
|
||||
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||||
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@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
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||||
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||||
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||||
@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
|
||||
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||||
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||||
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||||
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|
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|
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||||
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||||
|
||||
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|
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|
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||||
@@ -12,7 +12,7 @@
|
||||
|
||||
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|
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||||
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||||
+29
-29
@@ -10,7 +10,7 @@
|
||||
|
||||
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|
||||
|
||||
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|
||||
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|
||||
@@ -182,41 +182,41 @@
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 11 6 3 62 46 35 47 39 18 32 12 8 8 26 63 47 24 52 25 8 15 26 15 30 14</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 63 31 38 8 28 54 27 16 37 17 43 6 21 58 2 24 60 63 44 38 19 28 51 62 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 30 27 54 12 7 40 42 66 39 39 58 41 38 45 56 18 9 13 63 16 7 58 3 18 60</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 63 10 26 27 14 39 15 42 12 2 13 19 61 13 38 64 1 21 48 36 24 38 5 60 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 18 34 45 60 11 15 8 2 11 10 62 31 22 15 12 62 11 36 49 22 8 49 56 59 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 10 17 54 43 1 7 53 55 64 6 37 9 38 29 52 63 62 13 5 28 56 13 54 41 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 59 44 52 60 20 51 2 2 53 59 61 33 23 34 24 44 56 62 3 50 45 12 42 17 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 65 1 18 4 13 32 41 4 34 2 45 64 9 36 38 17 41 35 57 18 6 4 63 2 25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 63 42 61 46 22 21 21 10 46 12 31 47 53 64 9 27 12 7 30 25 15 61 52 20 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 46 53 39 38 54 61 58 12 58 39 21 27 35 66 46 59 57 13 43 30 29 60 51 25 35</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 22 4 56 20 5 18 18 22 9 21 50 9 58 38 59 44 46 11 41 55 55 5 14 56 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 53 63 33 20 5 31 32 10 1 51 46 2 28 24 40 10 13 26 55 12 49 54 16 43 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 51 37 60 27 49 23 42 63 5 60 7 23 4 37 47 22 52 45 65 56 11 38 17 36 12</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 9 47 25 14 1 56 38 66 42 53 19 51 10 34 16 11 15 62 31 40 22 63 49 32 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 45 6 48 5 58 57 7 56 46 13 58 65 15 21 7 42 8 5 6 6 28 29 4 26 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 3 56 3 60 61 63 63 56 65 16 21 40 57 23 16 47 58 61 21 32 9 60 3 17 62</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-23 B TRUE FALSE FALSE 51 M F35553 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-07-23 B TRUE FALSE FALSE 51 M F35553 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-07-16 D FALSE FALSE TRUE 78 M 241328 B_STPHY_CONS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-06-06 D FALSE TRUE FALSE 20 F 24D393 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-06-18 B TRUE FALSE FALSE 30 M 012595 B_CRYNB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-07-23 B TRUE FALSE FALSE 51 M F35553 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>, AMX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>,</span></span>
|
||||
|
||||
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|
||||
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|
||||
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|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
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|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
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|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
+1
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@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -172,9 +172,9 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.97178</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.031812</span>
|
||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.01957164</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.03994734</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
+1
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@@ -10,7 +10,7 @@
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||||
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||
+1
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@@ -10,7 +10,7 @@
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||||
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||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
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||||
|
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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||||
@@ -10,7 +10,7 @@
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||||
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||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
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||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
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|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
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||||
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||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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||||
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||||
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|
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+1
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -307,6 +307,8 @@
|
||||
<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
|
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<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
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<span class="r-in"><span></span></span>
|
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
@@ -314,7 +316,7 @@
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_rsi_values</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-7.png" alt="" width="700" height="433"></span>
|
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<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
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|
||||
@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
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|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
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|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
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|
||||
+17
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@@ -10,7 +10,7 @@
|
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|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -183,43 +183,42 @@
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.002 4 2 0.005 0.025 >=256 128 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 2 <=0.001 2 64 16 >=256 0.125 0.002 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.005 0.25 0.005 2 >=256 0.01 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 8 64 8 0.25 8 2 0.005 16 256 32 16 0.125</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] 0.125 64 32 0.25 256 4 1 0.125 32 0.5 0.025 128 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] 0.25 </span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 28 48 49 18 11 30 16 23 16 12 35 47 42 8 20 49 44 31 42 25 18 7 26 41 44</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 27 41 44 30 6 49 34 45 48 31 48 31 31 41 49 46 14 24 31 12 45 24 44 36 38</span>
|
||||
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R I I R S R S S I S I I S I R I R S I R S I S S R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I I R S S R S S S I I R I R I I S R R R S I S I S</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 0.002 128 2 0.0625 1 <=0.001 256 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 32 <=0.001 <=0.001 32 128 64 64 32 0.025 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 8 2 0.002 0.5 0.125 <=0.001 256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.25 0.125 0.002 4 2 8 32 0.0625 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.125 0.005 1 0.002 0.001 16 0.025 0.25 0.5 128 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 2 0.005 128 4 0.002 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 4 8 2 8 8 <=0.5 2 4 <=0.5 4 32 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] <=0.5 32 <=0.5 1 2 <=0.5 <=0.5 8 64 <=0.5 16 64 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=1 4 8 8 8 8 8 >=16 2 2 4 2 <=1 8 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] <=1 >=16 2 2 8 4 4 8 <=1 <=1 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 4 0.25 1 <=0.125 1 2 0.5 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 1 2 <=0.125 0.5 1 4 4 1 <=0.125</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.5 0.5 0.5 2 2 4 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.25 2 0.5 0.0625 8 0.25 0.25 0.125 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 2 0.125 0.0625 4 0.5 0.125 2 8 4 0.0625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.5 0.25 0.5 8 0.25 </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 38 25 31 29 9 27 9 16 47 41 43 32 19 14 38 18 28 11 8 42 43 22 46 18 28</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 42 30 13 25 19 37 49 26 38 8 46 40 23 25 44 11 40 13 22 34 15 36 47 49 49</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 15 14 17 11 15 17 16 15 17 14 12 15 14 13 16 12 13 12 12 12 16 12 15 14</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 14 17 16 15 16 15 11 16 16 15 15 13 13 15 11 15 15 15 17 13 11 15 17 11</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 21 18 23 25 23 16 15 19 19 19 25 27 27 17 21 21 23 18 22 25 27 25 18 15 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 20 25 18 16 15 19 16 21 23 19 25 18 16 16 16 18 16 27 17 27 23 22 17 19 19</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
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|
||||
@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -171,7 +171,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.01821464</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.06804385</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9020</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+1
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[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(patient_id = patients, gender = c(rep(\"M\", 135), rep(\"F\", 125)))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(\"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everyLine truncated
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[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(patient_id = patients, gender = c(rep(\"M\", 135), rep(\"F\", 125)))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(\"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everyLine truncated
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