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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9144</small>
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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="">1.8.2.9144</small>
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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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
@@ -408,42 +408,31 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-12-05</td>
<td align="center">E7</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2011-10-24</td>
<td align="center">V3</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-12-08</td>
<td align="center">T9</td>
<td align="center">2016-01-11</td>
<td align="center">K4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-04-10</td>
<td align="center">K10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-05-27</td>
<tr class="odd">
<td align="center">2014-07-11</td>
<td align="center">W3</td>
<td align="center">Hospital D</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
@@ -451,26 +440,37 @@ data set:</p>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-07-16</td>
<td align="center">M3</td>
<td align="center">Hospital D</td>
<tr class="even">
<td align="center">2011-04-14</td>
<td align="center">X5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-07-12</td>
<td align="center">V7</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-10-13</td>
<td align="center">U3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">2011-09-22</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
</tbody>
@@ -507,16 +507,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,401</td>
<td align="right">52.01%</td>
<td align="right">10,401</td>
<td align="right">52.01%</td>
<td align="right">10,503</td>
<td align="right">52.52%</td>
<td align="right">10,503</td>
<td align="right">52.52%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,599</td>
<td align="right">48.00%</td>
<td align="right">9,497</td>
<td align="right">47.49%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -629,9 +629,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co">#&gt; Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co">#&gt; 2</span></span>
<span><span class="co">#&gt; Including isolates from ICU.</span></span>
<span><span class="co">#&gt; =&gt; Found 12,354 'phenotype-based' first isolates (61.8% of total where a</span></span>
<span><span class="co">#&gt; =&gt; Found 12,333 'phenotype-based' first isolates (61.7% of total where a</span></span>
<span><span class="co">#&gt; microbial ID was available)</span></span></code></pre></div>
<p>So only 61.8% is suitable for resistance analysis! We can now filter
<p>So only 61.7% 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">
@@ -641,11 +641,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</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 12 354 isolates for analysis. Now our data looks
<p>So we end up with 12 333 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">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@@ -659,7 +659,7 @@ like:</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@@ -681,25 +681,9 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-12-05</td>
<td align="center">E7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</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">2</td>
<td align="center">2012-12-08</td>
<td align="center">T9</td>
<td align="center">Hospital A</td>
<td align="center">2011-10-24</td>
<td align="center">V3</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
@@ -711,11 +695,11 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-05-27</td>
<tr class="even">
<td align="left">3</td>
<td align="center">2014-07-11</td>
<td align="center">W3</td>
<td align="center">Hospital D</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@@ -727,54 +711,70 @@ like:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2017-07-16</td>
<td align="center">M3</td>
<td align="center">Hospital D</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">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">6</td>
<td align="center">2014-10-13</td>
<td align="center">U3</td>
<td align="center">Hospital D</td>
<td align="center">2011-09-22</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</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="even">
<td align="left">7</td>
<td align="center">2010-12-17</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</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">
<tr class="odd">
<td align="left">8</td>
<td align="center">2016-10-22</td>
<td align="center">K10</td>
<td align="center">Hospital B</td>
<td align="center">2010-01-14</td>
<td align="center">S8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</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="even">
<td align="left">10</td>
<td align="center">2015-08-01</td>
<td align="center">G9</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</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>
</tbody>
</table>
<p>Time for the analysis!</p>
@@ -808,8 +808,8 @@ readable:</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">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/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: 12,354<br>
Available: 12,354 (100%, NA: 0 = 0%)<br>
Length: 12,333<br>
Available: 12,333 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -834,33 +834,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,962</td>
<td align="right">48.26%</td>
<td align="right">5,962</td>
<td align="right">48.26%</td>
<td align="right">5,838</td>
<td align="right">47.34%</td>
<td align="right">5,838</td>
<td align="right">47.34%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,321</td>
<td align="right">26.88%</td>
<td align="right">9,283</td>
<td align="right">75.14%</td>
<td align="right">3,318</td>
<td align="right">26.90%</td>
<td align="right">9,156</td>
<td align="right">74.24%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,785</td>
<td align="right">14.45%</td>
<td align="right">11,068</td>
<td align="right">89.59%</td>
<td align="right">1,871</td>
<td align="right">15.17%</td>
<td align="right">11,027</td>
<td align="right">89.41%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,286</td>
<td align="right">10.41%</td>
<td align="right">12,354</td>
<td align="right">1,306</td>
<td align="right">10.59%</td>
<td align="right">12,333</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -881,14 +881,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@@ -909,93 +909,93 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-12-05</td>
<td align="center">E7</td>
<td align="center">2011-10-24</td>
<td align="center">V3</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-07-11</td>
<td align="center">W3</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">R</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">2010-01-14</td>
<td align="center">S8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-11-09</td>
<td align="center">P5</td>
<td align="center">Hospital D</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">2017-05-08</td>
<td align="center">Z4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</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="even">
<td align="center">2012-12-08</td>
<td align="center">T9</td>
<td align="center">2016-09-09</td>
<td align="center">I7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-05-27</td>
<td align="center">W3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</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="even">
<td align="center">2014-10-13</td>
<td align="center">U3</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</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>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-10-22</td>
<td align="center">K10</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">R</td>
<td align="center">I</td>
<td align="center">R</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="even">
<td align="center">2013-06-14</td>
<td align="center">Y4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</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">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@@ -1020,50 +1020,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2824</td>
<td align="center">1209</td>
<td align="center">1929</td>
<td align="center">5962</td>
<td align="center">2657</td>
<td align="center">1244</td>
<td align="center">1937</td>
<td align="center">5838</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1538</td>
<td align="center">1294</td>
<td align="center">3130</td>
<td align="center">5962</td>
<td align="center">1415</td>
<td align="center">1280</td>
<td align="center">3143</td>
<td align="center">5838</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2046</td>
<td align="center">1862</td>
<td align="center">2054</td>
<td align="center">5962</td>
<td align="center">1998</td>
<td align="center">1817</td>
<td align="center">2023</td>
<td align="center">5838</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2049</td>
<td align="center">1812</td>
<td align="center">2101</td>
<td align="center">5962</td>
<td align="center">1984</td>
<td align="center">1767</td>
<td align="center">2087</td>
<td align="center">5838</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">560</td>
<td align="center">278</td>
<td align="center">448</td>
<td align="center">1286</td>
<td align="center">561</td>
<td align="center">285</td>
<td align="center">460</td>
<td align="center">1306</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1286</td>
<td align="center">1286</td>
<td align="center">1306</td>
<td align="center">1306</td>
</tr>
</tbody>
</table>
@@ -1085,34 +1085,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2049</td>
<td align="center">1812</td>
<td align="center">2101</td>
<td align="center">5962</td>
<td align="center">1984</td>
<td align="center">1767</td>
<td align="center">2087</td>
<td align="center">5838</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">451</td>
<td align="center">389</td>
<td align="center">446</td>
<td align="center">1286</td>
<td align="center">435</td>
<td align="center">423</td>
<td align="center">448</td>
<td align="center">1306</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1163</td>
<td align="center">1016</td>
<td align="center">1142</td>
<td align="center">3321</td>
<td align="center">1143</td>
<td align="center">1003</td>
<td align="center">1172</td>
<td align="center">3318</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">1785</td>
<td align="center">1785</td>
<td align="center">1871</td>
<td align="center">1871</td>
</tr>
</tbody>
</table>
@@ -1144,7 +1144,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><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">%&gt;%</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">#&gt; [1] 0.5781124</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 0.5837996</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="cb26"><pre class="downlit sourceCode r">
@@ -1159,19 +1159,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5903060</td>
<td align="center">0.5860452</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5759064</td>
<td align="center">0.5836969</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5773087</td>
<td align="center">0.5804851</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5644320</td>
<td align="center">0.5831363</td>
</tr>
</tbody>
</table>
@@ -1196,23 +1196,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5903060</td>
<td align="center">3693</td>
<td align="center">0.5860452</td>
<td align="center">3626</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5759064</td>
<td align="center">4275</td>
<td align="center">0.5836969</td>
<td align="center">4355</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5773087</td>
<td align="center">1895</td>
<td align="center">0.5804851</td>
<td align="center">1814</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5644320</td>
<td align="center">2491</td>
<td align="center">0.5831363</td>
<td align="center">2538</td>
</tr>
</tbody>
</table>
@@ -1237,27 +1237,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6764509</td>
<td align="center">0.6476015</td>
<td align="center">0.8901375</td>
<td align="center">0.6682083</td>
<td align="center">0.6425146</td>
<td align="center">0.8795820</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6516330</td>
<td align="center">0.6531882</td>
<td align="center">0.8833593</td>
<td align="center">0.6477795</td>
<td align="center">0.6569678</td>
<td align="center">0.8843798</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6591388</td>
<td align="center">0.6561277</td>
<td align="center">0.8858777</td>
<td align="center">0.6564195</td>
<td align="center">0.6467752</td>
<td align="center">0.8758288</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4829132</td>
<td align="center">0.4820951</td>
<td align="center">0.0000000</td>
<td align="center">0.4829132</td>
<td align="center">0.4820951</td>
</tr>
</tbody>
</table>
@@ -1285,23 +1285,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">59.0%</td>
<td align="right">36.6%</td>
<td align="right">58.6%</td>
<td align="right">36.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">57.6%</td>
<td align="right">35.7%</td>
<td align="right">58.4%</td>
<td align="right">37.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.7%</td>
<td align="right">36.6%</td>
<td align="right">58.0%</td>
<td align="right">35.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.4%</td>
<td align="right">34.5%</td>
<td align="right">58.3%</td>
<td align="right">36.0%</td>
</tr>
</tbody>
</table>
@@ -1417,16 +1417,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</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">#&gt; Class 'mic'</span></span>
<span><span class="co">#&gt; [1] 0.0625 0.001 0.01 0.125 0.01 0.01 0.025 32 0.25 0.025 </span></span>
<span><span class="co">#&gt; [11] 0.25 4 0.01 0.001 0.005 16 2 0.01 0.025 0.025 </span></span>
<span><span class="co">#&gt; [21] 0.01 0.005 0.0625 0.01 0.005 0.001 0.01 0.002 0.01 &gt;=256 </span></span>
<span><span class="co">#&gt; [31] 0.025 0.025 0.005 4 0.005 0.001 0.5 64 0.025 4 </span></span>
<span><span class="co">#&gt; [41] 0.0625 &gt;=256 1 0.125 16 32 0.01 0.01 64 64 </span></span>
<span><span class="co">#&gt; [51] 1 0.25 0.25 0.125 128 0.002 64 0.125 16 128 </span></span>
<span><span class="co">#&gt; [61] 0.01 0.01 0.01 128 0.0625 8 0.01 0.5 16 1 </span></span>
<span><span class="co">#&gt; [71] 0.005 128 0.002 0.125 2 16 0.01 0.25 1 2 </span></span>
<span><span class="co">#&gt; [81] 0.001 4 0.002 8 0.25 8 0.002 16 0.01 128 </span></span>
<span><span class="co">#&gt; [91] 1 128 0.125 0.5 0.01 0.025 0.5 32 0.0625 0.002</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 16 0.0625 0.0625 0.002 32 1 1 0.001 1 0.025 </span></span>
<span><span class="co">#&gt; [11] 32 2 256 0.25 64 0.25 4 0.025 256 0.25 </span></span>
<span><span class="co">#&gt; [21] 0.125 0.005 1 4 16 16 2 2 1 0.0625</span></span>
<span><span class="co">#&gt; [31] 0.125 0.025 8 0.002 16 0.0625 0.5 256 128 0.001 </span></span>
<span><span class="co">#&gt; [41] 8 1 0.01 0.001 0.01 64 16 32 128 64 </span></span>
<span><span class="co">#&gt; [51] 256 0.01 0.01 0.001 0.002 64 0.01 0.001 0.01 0.125 </span></span>
<span><span class="co">#&gt; [61] 0.01 0.125 128 0.01 64 8 32 64 2 1 </span></span>
<span><span class="co">#&gt; [71] 0.005 0.125 2 0.025 0.125 0.01 4 0.002 0.005 2 </span></span>
<span><span class="co">#&gt; [81] 4 64 8 0.002 0.125 256 16 1 2 0.5 </span></span>
<span><span class="co">#&gt; [91] 1 0.0625 32 0.001 2 0.025 0.002 0.002 0.25 1</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><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>
@@ -1460,10 +1460,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</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>
<span><span class="va">disk_values</span></span>
<span><span class="co">#&gt; Class 'disk'</span></span>
<span><span class="co">#&gt; [1] 27 26 31 31 27 28 21 17 30 29 22 24 19 27 22 31 19 17 23 27 18 29 24 26 19</span></span>
<span><span class="co">#&gt; [26] 30 28 22 30 24 19 27 27 20 25 22 19 19 26 17 27 29 27 26 27 27 30 19 27 21</span></span>
<span><span class="co">#&gt; [51] 24 24 19 23 21 18 30 22 28 22 26 26 21 19 31 19 17 24 30 28 25 22 23 30 24</span></span>
<span><span class="co">#&gt; [76] 23 21 26 30 23 28 24 27 22 28 31 21 30 23 30 26 17 28 17 29 19 20 28 28 27</span></span></code></pre></div>
<span><span class="co">#&gt; [1] 29 27 23 23 27 24 27 29 26 18 17 28 21 27 22 20 17 18 21 23 19 25 30 22 18</span></span>
<span><span class="co">#&gt; [26] 21 25 27 17 27 22 28 18 27 21 29 19 28 24 29 27 26 18 29 30 25 24 25 22 17</span></span>
<span><span class="co">#&gt; [51] 30 30 29 21 29 19 21 26 17 31 23 25 27 29 19 18 18 30 18 24 18 26 27 21 25</span></span>
<span><span class="co">#&gt; [76] 30 26 19 17 19 27 31 19 19 23 29 30 22 19 30 17 24 31 26 29 19 20 23 25 30</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
articles/MDR.html
+29 -29
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
@@ -385,19 +385,19 @@ names or codes, this would have worked exactly the same way:</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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 I I R R S I</span></span>
<span><span class="co">#&gt; 2 R R S S R R</span></span>
<span><span class="co">#&gt; 3 R R S I I R</span></span>
<span><span class="co">#&gt; 4 I R R S I R</span></span>
<span><span class="co">#&gt; 5 I I R I R R</span></span>
<span><span class="co">#&gt; 6 R I I I S R</span></span>
<span><span class="co">#&gt; 1 I I R R S S</span></span>
<span><span class="co">#&gt; 2 I R I I R S</span></span>
<span><span class="co">#&gt; 3 S S R S I I</span></span>
<span><span class="co">#&gt; 4 I S S S S R</span></span>
<span><span class="co">#&gt; 5 S S I I I I</span></span>
<span><span class="co">#&gt; 6 R S R R S S</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 6 S</span></span></code></pre></div>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 R</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">
@@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
<td align="right">3218</td>
<td align="right">64.36%</td>
<td align="right">3218</td>
<td align="right">64.36%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">959</td>
<td align="right">19.18%</td>
<td align="right">4155</td>
<td align="right">83.10%</td>
<td align="right">991</td>
<td align="right">19.82%</td>
<td align="right">4209</td>
<td align="right">84.18%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">479</td>
<td align="right">9.58%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4651</td>
<td align="right">93.02%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">256</td>
<td align="right">5.12%</td>
<td align="right">4890</td>
<td align="right">97.80%</td>
<td align="right">241</td>
<td align="right">4.82%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">110</td>
<td align="right">2.20%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">1.8.2.9144</small>
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@@ -142,7 +142,7 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9144" id="amr-1829144">AMR 1.8.2.9144<a class="anchor" aria-label="anchor" href="#amr-1829144"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9145" id="amr-1829145">AMR 1.8.2.9145<a class="anchor" aria-label="anchor" href="#amr-1829145"></a></h2>
<p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
<p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
<p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
@@ -156,32 +156,32 @@
<li>Now available in 20 languages</li>
<li>Many small bug fixes</li>
</ul><div class="section level3">
<h3 id="new-1-8-2-9144">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9144"></a></h3>
<h3 id="new-1-8-2-9145">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9145"></a></h3>
<div class="section level4">
<h4 id="sir-vs-rsi-1-8-2-9144">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9144"></a></h4>
<h4 id="sir-vs-rsi-1-8-2-9145">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9145"></a></h4>
<p>For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR.</p>
<p>While existing functions such as <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>, <code><a href="../reference/AMR-deprecated.html">rsi_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">ggplot_rsi()</a></code> still work, their replacements <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/proportion.html">sir_df()</a></code>, <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set <code>rsi_translation</code> is now called <code>clinical_breakpoints</code> to better reflect its content.</p>
<p>The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024.</p>
</div>
<div class="section level4">
<h4 id="new-antibiogram-function-1-8-2-9144">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9144"></a></h4>
<h4 id="new-antibiogram-function-1-8-2-9145">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9145"></a></h4>
<p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
<p>The help page for <code><a href="../reference/antibiogram.html">antibiogram()</a></code> extensively elaborates on use cases, and <code><a href="../reference/antibiogram.html">antibiogram()</a></code> also supports printing in R Markdown and Quarto, with support for 20 languages.</p>
<p>Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.</p>
</div>
<div class="section level4">
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9144">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9144"></a></h4>
<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9145">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9145"></a></h4>
<p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
<p>With the new arguments <code>include_PKPD</code> (default: <code>TRUE</code>) and <code>include_screening</code> (default: <code>FALSE</code>), users can now specify whether breakpoints for screening and from the PK/PD table should be included when interpreting MICs and disks diffusion values. These options can be set globally, which can be read in <a href="https://msberends.github.io/AMR/reference/AMR-options.html">our new manual</a>.</p>
<p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
</div>
<div class="section level4">
<h4 id="supported-languages-1-8-2-9144">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9144"></a></h4>
<h4 id="supported-languages-1-8-2-9145">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9145"></a></h4>
<p>We added support for the following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user’s system language.</p>
<p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 20 languages in total, and according to download stats used in almost all countries in the world!</p>
</div>
<div class="section level4">
<h4 id="microbiological-taxonomy-1-8-2-9144">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9144"></a></h4>
<h4 id="microbiological-taxonomy-1-8-2-9145">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9145"></a></h4>
<p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
<p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
<p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
@@ -205,7 +205,7 @@
<li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
</ul></div>
<div class="section level4">
<h4 id="antibiotic-agents-and-selectors-1-8-2-9144">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9144"></a></h4>
<h4 id="antibiotic-agents-and-selectors-1-8-2-9145">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9145"></a></h4>
<p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
<p>The <code>antibiotics</code> data set was greatly updated:</p>
<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@@ -217,14 +217,14 @@
</ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
</div>
<div class="section level4">
<h4 id="antiviral-agents-1-8-2-9144">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9144"></a></h4>
<h4 id="antiviral-agents-1-8-2-9145">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9145"></a></h4>
<p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
<ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
<li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
<li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
</ul></div>
<div class="section level4">
<h4 id="other-new-functions-1-8-2-9144">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9144"></a></h4>
<h4 id="other-new-functions-1-8-2-9145">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9145"></a></h4>
<ul><li>Function <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
<li>Function <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.sir.html">as.sir()</a></code> (previously <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.sir.html">as.sir()</a></code> was run.</li>
@@ -233,8 +233,15 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="changes-1-8-2-9144">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9144"></a></h3>
<ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">sir_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<h3 id="changes-1-8-2-9145">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9145"></a></h3>
<ul><li>
<code><a href="../reference/get_episode.html">get_episode()</a></code> (and its wrapper <code><a href="../reference/get_episode.html">is_new_episode()</a></code>):
<ul><li>Gained an argument <code>new_after_days</code> to determine episodes based on epidemic periods</li>
<li>Fix for working with <code>NA</code> values</li>
<li>Fix for unsorted dates of length 2</li>
<li>Now returns class <code>integer</code> instead of <code>numeric</code> since they are always whole numbers</li>
</ul></li>
<li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">sir_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://sfirke.github.io/janitor/reference/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
<li>All data sets in this package are now a <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported, even if they do not support <code>tibble</code>s.</li>
@@ -272,12 +279,10 @@
<li>Cleaning columns with <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
<li>Fix for using <code><a href="../reference/g.test.html">g.test()</a></code> with zeroes in a 2x2 table</li>
<li>
<code><a href="../reference/get_episode.html">get_episode()</a></code> now returns class <code>integer</code> instead of <code>numeric</code> since they are always whole numbers</li>
<li>
<code>mo_synonyns()</code> now contains the scientific reference as names</li>
</ul></div>
<div class="section level3">
<h3 id="other-1-8-2-9144">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9144"></a></h3>
<h3 id="other-1-8-2-9145">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9145"></a></h3>
<ul><li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, and Anita Williams as contributors, to thank them for their valuable input</li>
<li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
pkgdown.yml
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@@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2023-02-24T09:36Z
last_built: 2023-02-24T16:10Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
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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="">1.8.2.9144</small>
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@@ -10,7 +10,7 @@
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@@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German,
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
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reference/age.html
+11 -11
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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="">1.8.2.9144</small>
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@@ -205,16 +205,16 @@
<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">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1940-12-29 82 82.15616 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1987-01-19 36 36.09863 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1975-05-13 47 47.78630 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1987-01-10 36 36.12329 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1965-10-22 57 57.34247 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1941-11-09 81 81.29315 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1942-10-07 80 80.38356 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1970-01-05 53 53.13699 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1954-12-23 68 68.17260 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1979-04-28 43 43.82740 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1951-07-26 71 71.58356 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1957-01-31 66 66.06575 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1986-04-15 36 36.86301 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1942-10-08 80 80.38082 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-02-25 90 90.99726 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1986-05-12 36 36.78904 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1986-10-24 36 36.33699 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1969-12-26 53 53.16438 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1941-07-07 81 81.63562 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1984-12-17 38 38.18904 15</span>
</code></pre></div>
</div>
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
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@@ -10,7 +10,7 @@
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@@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-24 <span style="color: #949494;">09:37:18</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-24 <span style="color: #949494;">09:37:17</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-24 <span style="color: #949494;">09:37:17</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-24 <span style="color: #949494;">09:37:17</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-24 <span style="color: #949494;">09:37:12</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-24 <span style="color: #949494;">09:37:12</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-24 <span style="color: #949494;">09:37:12</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-24 <span style="color: #949494;">09:37:12</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-24 <span style="color: #949494;">09:37:12</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-24 <span style="color: #949494;">09:37:12</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-24 <span style="color: #949494;">16:11:48</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-24 <span style="color: #949494;">16:11:47</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-24 <span style="color: #949494;">16:11:47</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-24 <span style="color: #949494;">16:11:47</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-24 <span style="color: #949494;">16:11:40</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;, ab_considered &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mo_considered &lt;lgl&gt;, breakpoint_S &lt;lgl&gt;, breakpoint_R &lt;lgl&gt;,</span></span>
reference/atc_online.html
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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Determine (Clinical) Episodes</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Determine (Clinical or Epidemic) Episodes</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/get_episode.R" class="external-link"><code>R/get_episode.R</code></a></small>
<div class="d-none name"><code>get_episode.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while the <code>is_new_episode()</code> function returns <code>TRUE</code> for every new <code>get_episode()</code> index, and is thus equal to <code>!duplicated(get_episode(...))</code>.</p>
<p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while the <code>is_new_episode()</code> function returns <code>TRUE</code> for every new <code>get_episode()</code> index. Both absolute and relative episode determination are supported.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span>, episode_days <span class="op">=</span> <span class="cn">NULL</span>, case_free_days <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">x</span>, episode_days <span class="op">=</span> <span class="cn">NULL</span>, case_free_days <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -160,7 +160,11 @@
<dt>episode_days</dt>
<dd><p>required episode length in days, can also be less than a day or <code>Inf</code>, see <em>Details</em></p></dd>
<dd><p>episode length in days, can also be less than a day or <code>Inf</code>, see <em>Details</em></p></dd>
<dt>case_free_days</dt>
<dd><p>length in days after which new episode will start, can also be less than a day or <code>Inf</code>, see <em>Details</em></p></dd>
<dt>...</dt>
@@ -176,9 +180,28 @@
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The functions <code>get_episode()</code> and <code>is_new_episode()</code> differ in this way when setting <code>episode_days</code> to 365:</p><table class="table table"><tr><td>person_id</td><td>date</td><td><code>get_episode()</code></td><td><code>is_new_episode()</code></td></tr><tr><td>A</td><td>2019-01-01</td><td>1</td><td>TRUE</td></tr><tr><td>A</td><td>2019-03-01</td><td>1</td><td>FALSE</td></tr><tr><td>A</td><td>2021-01-01</td><td>2</td><td>TRUE</td></tr><tr><td>B</td><td>2008-01-01</td><td>1</td><td>TRUE</td></tr><tr><td>B</td><td>2008-01-01</td><td>1</td><td>FALSE</td></tr><tr><td>C</td><td>2020-01-01</td><td>1</td><td>TRUE</td></tr></table><p>Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least <code>episode_days</code> days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least <code>episode_days</code> days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.</p>
<p>Episodes can be determined in two ways: absolute and relative.</p><ol><li><p>Absolute</p>
<p>This method uses <code>episode_days</code> to define an episode length in days, after which a new episode will start. A common use case in AMR data analysis is microbial epidemiology: episodes of <em>S. aureus</em> bacteraemia in ICU patients for example. The episode length could then be 30 days, so that new <em>S. aureus</em> isolates after an ICU episode of 30 days will be considered a different (or new) episode.</p>
<p>Thus, this method counts <strong>since the start of the previous episode</strong>.</p></li>
<li><p>Relative</p>
<p>This method uses <code>case_free_days</code> to quantify the duration of (inter-epidemic) intervals, after which a new episode will start. A common use case is infectious disease epidemiology: episodes of norovirus outbreaks in a hospital for example. The case-free period could then be 14 days, so that new norovirus cases after that time will be considered a different (or new) episode.</p>
<p>Thus, this methods counts <strong>since the last case in the previous episode</strong>.</p></li>
</ol><p>In a table:</p><table class="table table"><tr><td>Date</td><td>Using <code>episode_days = 7</code></td><td>Using <code>case_free_days = 7</code></td></tr><tr><td>2023-01-01</td><td>1</td><td>1</td></tr><tr><td>2023-01-02</td><td>1</td><td>1</td></tr><tr><td>2023-01-05</td><td>1</td><td>1</td></tr><tr><td>2023-01-08</td><td>2<code>*</code></td><td>1</td></tr><tr><td>2023-02-21</td><td>3</td><td>2<code>**</code></td></tr><tr><td>2023-02-22</td><td>3</td><td>2</td></tr><tr><td>2023-02-23</td><td>3</td><td>2</td></tr><tr><td>2023-02-24</td><td>3</td><td>2</td></tr><tr><td>2023-03-01</td><td>4</td><td>2</td></tr></table><p><code>*</code> This marks the start of a new episode, because 8 January 2023 is more than 7 days since the start of the previous episode (1 January 2023). <br><code>**</code> This marks the start of a new episode, because 21 January 2023 is more than 7 days since the last case in the previous episode (8 January 2023).</p><div class="section">
<h3 id="difference-between-get-episode-and-is-new-episode-">Difference between <code>get_episode()</code> and <code>is_new_episode()</code><a class="anchor" aria-label="anchor" href="#difference-between-get-episode-and-is-new-episode-"></a></h3>
<p>The <code>get_episode()</code> function returns the index number of the episode, so all cases/patients/isolates in the first episode will have the number 1, all cases/patients/isolates in the second episode will have the number 2, etc.</p>
<p>The <code>is_new_episode()</code> function returns <code>TRUE</code> for every new <code>get_episode()</code> index, and is thus equal to <code>!duplicated(get_episode(...))</code>.</p>
<p>To specify, when setting <code>episode_days = 365</code> (using method 1 as explained above), this is how the two functions differ:</p><table class="table table"><tr><td>patient</td><td>date</td><td><code>get_episode()</code></td><td><code>is_new_episode()</code></td></tr><tr><td>A</td><td>2019-01-01</td><td>1</td><td>TRUE</td></tr><tr><td>A</td><td>2019-03-01</td><td>1</td><td>FALSE</td></tr><tr><td>A</td><td>2021-01-01</td><td>2</td><td>TRUE</td></tr><tr><td>B</td><td>2008-01-01</td><td>1</td><td>TRUE</td></tr><tr><td>B</td><td>2008-01-01</td><td>1</td><td>FALSE</td></tr><tr><td>C</td><td>2020-01-01</td><td>1</td><td>TRUE</td></tr></table></div>
<div class="section">
<h3 id="other">Other<a class="anchor" aria-label="anchor" href="#other"></a></h3>
<p>The <code><a href="first_isolate.html">first_isolate()</a></code> function is a wrapper around the <code>is_new_episode()</code> function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.</p>
<p>The <code>dplyr</code> package is not required for these functions to work, but these episode functions do support <a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">variable grouping</a> and work conveniently inside <code>dplyr</code> verbs such as <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>.</p>
</div>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -187,34 +210,61 @@
<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="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># difference between absolute and relative determination of episodes:</span></span></span>
<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>dates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="st">"2021-01-01"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-01-02"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-01-05"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-01-08"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-21"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-22"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-23"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-24"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-03-01"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-03-01"</span></span></span>
<span class="r-in"><span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span><span class="op">$</span><span class="va">absolute</span> <span class="op">&lt;-</span> <span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">dates</span>, episode_days <span class="op">=</span> <span class="fl">7</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span><span class="op">$</span><span class="va">relative</span> <span class="op">&lt;-</span> <span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">dates</span>, case_free_days <span class="op">=</span> <span class="fl">7</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> dates absolute relative</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 2021-01-01 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2021-01-02 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 2021-01-05 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 2021-01-08 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 2021-02-21 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 2021-02-22 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 2021-02-23 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 2021-02-24 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 2021-03-01 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 2021-03-01 4 2</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
<span class="r-in"><span><span class="co"># See ?example_isolates</span></span></span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</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">100</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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 9 22 13 21 3 23 7 38 25 45 23 26 10 3 30 40 14 18 36 16 33 13 34 30 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 49 48 33 34 29 27 4 14 48 47 2 37 18 11 49 5 38 8 41 11 41 36 19 43 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 25 24 28 11 5 12 44 19 20 4 42 27 2 44 27 29 3 13 15 35 20 39 18 1 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 2 47 6 15 14 32 17 29 44 22 36 27 9 15 9 11 31 17 21 17 22 46 12 18 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 51 2 6 10 25 14 44 49 31 26 32 13 41 22 44 7 38 44 22 50 14 24 28 35 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 42 15 40 3 20 37 40 50 26 19 48 46 9 8 1 29 47 23 47 47 2 24 6 14 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 6 45 34 22 1 2 9 43 4 16 38 42 17 30 35 8 26 5 12 40 9 7 15 35 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 32 38 17 16 18 36 11 25 51 22 20 28 1 39 21 20 23 27 33 48 43 7 36 14 19</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE 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">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-15 426426 67 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-08-14 785317 51 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-10-22 718963 82 M ICU B_STPHY_EPDR R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;,</span></span>
@@ -249,19 +299,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [100]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 059414 2006-07-21 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 066601 2013-10-30 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 080086 2010-08-08 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 0E2483 2007-05-29 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 116866 2011-11-07 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 130252 2002-04-08 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 1343BD 2016-04-02 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1435C8 2004-03-03 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 180928 2008-06-14 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 189363 2004-06-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 004531 2013-12-02 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 023456 2009-11-02 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 023456 2009-11-02 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 04C169 2012-07-18 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 062027 2015-09-21 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 077922 2017-02-02 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 092034 2006-06-12 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 0C0688 2014-09-05 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 0E2483 2007-05-29 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 151041 2006-02-10 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -275,19 +325,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [97]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2006-07-21 059414 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2013-10-30 066601 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2010-08-08 080086 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2011-11-07 116866 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2002-04-08 130252 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2016-04-02 1343BD 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2004-03-03 1435C8 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-06-14 180928 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2004-06-22 189363 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-12-02 004531 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-11-02 023456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2009-11-02 023456 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2012-07-18 04C169 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2015-09-21 062027 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2017-02-02 077922 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2006-06-12 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2014-09-05 0C0688 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2006-02-10 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -303,9 +353,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 65 13 38 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 29 12 21 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 4 3 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 63 14 40 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 28 10 21 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 5 6 6</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@@ -334,19 +384,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 4047F6 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 7F8445 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A87231 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 532360 B_PSDMN_AERG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 426426 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 942999 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 1435C8 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 997433 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 982666 B_STRPT_DYSG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 3B8892 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 5DB1C8 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B30560 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 728932 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 619705 B_KLBSL_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> AB0003 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 7D4209 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D07D73 B_STRPT_PYGN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> BF4515 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> BC9909 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 982666 B_STRPT_DYSG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
reference/ggplot_pca.html
+1 -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="">1.8.2.9144</small>
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reference/ggplot_sir.html
+1 -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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reference/guess_ab_col.html
+1 -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/index.html
+2 -2
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
@@ -273,7 +273,7 @@
<code><a href="get_episode.html">get_episode()</a></code> <code><a href="get_episode.html">is_new_episode()</a></code>
</dt>
<dd>Determine (Clinical) Episodes</dd>
<dd>Determine (Clinical or Epidemic) Episodes</dd>
</dl><dl><dt>
<code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code>
reference/intrinsic_resistant.html
+1 -1
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/italicise_taxonomy.html
+1 -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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reference/join.html
+1 -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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reference/key_antimicrobials.html
+1 -1
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/kurtosis.html
+3 -3
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
@@ -182,9 +182,9 @@
<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">#&gt;</span> [1] 3.038382</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.965401</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">#&gt;</span> [1] 0.0601673</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.03055707</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/like.html
+1 -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="">1.8.2.9144</small>
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+1 -1
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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="">1.8.2.9144</small>
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reference/mean_amr_distance.html
+37 -36
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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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</small>
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@@ -201,30 +201,31 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R I I R R S R I R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S I I R I I R I R</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.7745967 0.7745967 -1.1618950 -1.1618950 0.7745967 0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.1618950 0.7745967 -1.1618950 0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.621059 -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] 1.449138 -0.621059 1.449138</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 32 0.5 16 0.005 &gt;=64 1 0.01 2 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.5 0.0625 &lt;=0.001 &gt;=128 0.5 32 &gt;=128 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.33109450 1.15548346 0.08719632 0.97743560 -1.09572804 1.33353132</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.26524418 -0.91768018 0.44329203 -0.91768018</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.90187954 -0.05159359 -0.50356433 -1.40235097 1.15366171 -0.05159359</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.85234788 1.15366171 -1.25169406 1.00300479</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.33109450 1.15548346 0.08719632 0.97743560 -1.09572804 1.33353132</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.26524418 -0.91768018 0.44329203 -0.91768018</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.90187954 -0.05159359 -0.50356433 -1.40235097 1.15366171 -0.05159359</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.85234788 1.15366171 -1.25169406 1.00300479</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 49 45 9 48 46 49 9 12 44 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 31 43 47 11 50 40 41 6 40 11</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.7291669 0.5065205 -1.4972970 0.6735053 0.5621821 0.7291669</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.4972970 -1.3303122 0.4508589 0.6735053</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06075813 0.66833944 0.91137196 -1.27592075 1.09364635 0.48606505</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.54682318 -1.57971140 0.48606505 -1.27592075</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -234,22 +235,22 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 29 &lt;=0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 24 &lt;=0.25 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 23 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 21 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 23 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 19 &gt;=8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 23 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 21 0.5 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 28 &lt;=0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 30 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 23 &lt;=0.25 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 22 &lt;=0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 22 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 29 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 25 &gt;=4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 17 0.5 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 29 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 19 0.5 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 24 1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 22 0.5 2</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.03951484 -0.73916397 -0.30108900 -0.07342681 -0.30108900 0.07678785</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.42484629 0.08146823 -0.02813789 0.82028946</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.6549761 -0.4877892 0.2461508 0.2294569 0.3737749 -0.4180608</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8678531 0.1870373 -0.0197123 -0.3237347</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -265,17 +266,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C I 23 1 1 -0.30108900 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E S 23 1 1 -0.30108900 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 D I 21 2 2 -0.07342681 0.2276622</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 I I 28 &lt;=0.25 2 -0.02813789 0.2729511</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A S 29 &lt;=0.25 2 0.03951484 0.3406038</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 19 &gt;=8 2 0.07678785 0.3778768</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 H I 21 0.5 &gt;=8 0.08146823 0.3825572</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B S 24 &lt;=0.25 &lt;=0.5 -0.73916397 0.4380750</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 G S 23 4 4 0.42484629 0.7259353</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 30 0.5 1 0.82028946 1.1213785</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 22 2 1 0.2461508 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D S 29 2 1 0.2294569 0.01669387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H R 19 0.5 &gt;=4 0.1870373 0.05911349</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E R 25 &gt;=4 0.5 0.3737749 0.12762412</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I R 24 1 0.5 -0.0197123 0.26586311</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 J I 22 0.5 2 -0.3237347 0.56988550</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 29 &gt;=4 1 0.8678531 0.62170227</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 F I 17 0.5 &gt;=4 -0.4180608 0.66421164</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B S 22 &lt;=0.25 2 -0.4877892 0.73393999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 A S 23 &lt;=0.25 1 -0.6549761 0.90112686</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
reference/microorganisms.codes.html
+1 -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/microorganisms.html
+1 -1
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/mo_matching_score.html
+1 -1
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/mo_property.html
+1 -1
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/mo_source.html
+1 -1
View File
@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/pca.html
+1 -1
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/plot-1.png
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reference/plot.html
+1 -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/proportion.html
+1 -1
View File
@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/random.html
+17 -17
View File
@@ -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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
@@ -193,42 +193,42 @@
<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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 0.005 32 32 0.002 0.25 64 32 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 128 &lt;=0.001 &lt;=0.001 &lt;=0.001 0.25 0.005 &gt;=256 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 64 8 &gt;=256 0.025 4 0.125 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 1 0.125 &gt;=256 32 0.005 0.25 0.25 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 32 64 0.125 32 4 0.0625 16 &lt;=0.001 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 1 32 0.125 2 16 0.5 </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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 37 42 49 34 38 41 43 38 18 20 50 28 38 29 41 41 11 17 11 43 30 36 11 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 26 28 25 20 42 41 9 45 22 49 25 50 32 23 20 23 41 46 28 46 40 48 37 24</span>
<span class="r-in"><span><span class="fu">random_sir</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">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R R R S R R I I R I I R S S S S S S S I R R I I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S R R S S R R R I I S S I I I R I I R I R R 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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 0.0625 &gt;=128 &lt;=0.001 64 0.025 &gt;=128 0.002 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 0.25 0.0625 64 16 4 0.025 0.25 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] &gt;=128 16 0.5 &gt;=128 2 16 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001 32 128 128 8 4 0.25 0.005 0.01 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.002 0.01 0.25 0.002 0.025 1 4 0.25 16 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 128 8 0.5 0.0625 16 </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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=1 2 2 &gt;=32 &lt;=1 8 2 16 16 &lt;=1 8 &lt;=1 &lt;=1 16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 8 8 &gt;=32 4 &lt;=1 &lt;=1 8 &lt;=1 &lt;=1 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 16 0.5 0.5 &gt;=32 8 8 1 8 &gt;=32 &gt;=32 2 0.5 0.5 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 2 0.5 4 2 1 0.5 &gt;=32 2 0.5 0.25</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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.025 1 0.0625 0.25 0.5 2 16 16 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 8 0.25 1 1 8 4 0.0625 0.025 16 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.025 0.25 0.5 0.5 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 1 0.25 2 &lt;=0.125 2 0.25 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 4 &lt;=0.125 0.25 4 0.25 0.5 2 &lt;=0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 1 1 0.25 &lt;=0.125 0.5 &lt;=0.125</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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 26 47 32 16 38 25 17 14 11 15 35 50 49 36 35 31 46 24 45 13 15 10 36 17 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 41 46 50 12 9 33 34 12 50 35 19 12 41 34 13 48 10 42 16 20 10 49 29 17 42</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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 14 17 11 11 13 12 11 12 14 13 15 15 14 15 17 11 14 12 13 12 14 12 14 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 13 11 16 16 14 14 12 13 17 17 16 13 13 13 15 15 17 13 17 15 11 12 16 12</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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 25 25 25 17 27 23 17 19 15 23 21 25 23 20 18 19 18 26 18 16 21 17 22 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 23 25 25 19 23 18 25 16 17 15 22 24 15 22 17 15 26 25 25 21 25 22 16 27</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
reference/resistance_predict.html
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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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
reference/skewness.html
+2 -2
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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="">1.8.2.9144</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9145</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">
@@ -181,7 +181,7 @@ 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">#&gt;</span> [1] -0.009588953</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.07241631</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9144</small>
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search.json
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@@ -1 +1 @@
[{"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 SIR 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-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
[{"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 SIR 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-everything-together","dir":"Articles","previous_headings":"CreatLine truncated