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</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 June 2020</h4>
<h4 class="date">22 June 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -195,7 +195,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 17 June 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 22 June 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -226,21 +226,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-06-17</td>
<td align="center">2020-06-22</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2020-06-17</td>
<td align="center">2020-06-22</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2020-06-17</td>
<td align="center">2020-06-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -336,71 +336,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-09-10</td>
<td align="center">V9</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-09-21</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-05-27</td>
<td align="center">U4</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-01-03</td>
<td align="center">I8</td>
<td align="center">Hospital B</td>
<td align="center">2014-04-15</td>
<td align="center">I4</td>
<td align="center">Hospital D</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-02-09</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-06-08</td>
<td align="center">2013-12-16</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-09-29</td>
<td align="center">T5</td>
<td align="center">Hospital A</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-08-23</td>
<td align="center">Z9</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-01-14</td>
<td align="center">N4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-01-31</td>
<td align="center">N1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -432,16 +432,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,319</td>
<td align="right">51.60%</td>
<td align="right">10,319</td>
<td align="right">51.60%</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
<td align="right">10,328</td>
<td align="right">51.64%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,681</td>
<td align="right">48.41%</td>
<td align="right">9,672</td>
<td align="right">48.36%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -481,7 +481,7 @@ Longest: 1</p>
<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
<span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span></pre></body></html></div>
<p>So only 28.2% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">first</span> <span class="kw">==</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -491,7 +491,7 @@ Longest: 1</p>
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient A2, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient N3, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -507,10 +507,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-14</td>
<td align="center">A2</td>
<td align="center">2010-03-10</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -518,8 +518,8 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-19</td>
<td align="center">A2</td>
<td align="center">2010-05-11</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -529,21 +529,21 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-08-09</td>
<td align="center">A2</td>
<td align="center">2010-05-17</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-12-29</td>
<td align="center">A2</td>
<td align="center">2010-05-18</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -551,8 +551,8 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-02-03</td>
<td align="center">A2</td>
<td align="center">2010-07-30</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -562,62 +562,62 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-15</td>
<td align="center">A2</td>
<td align="center">2010-09-15</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-22</td>
<td align="center">A2</td>
<td align="center">2010-10-06</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-06-10</td>
<td align="center">A2</td>
<td align="center">2010-11-30</td>
<td align="center">N3</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-20</td>
<td align="center">A2</td>
<td align="center">2011-01-27</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-08-06</td>
<td align="center">A2</td>
<td align="center">2011-01-30</td>
<td align="center">N3</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb18"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">keyab</span> <span class="kw">=</span> <span class="fu"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(<span class="no">.</span>)) <span class="kw">%&gt;%</span>
@ -643,10 +643,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-14</td>
<td align="center">A2</td>
<td align="center">2010-03-10</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -655,95 +655,95 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-19</td>
<td align="center">A2</td>
<td align="center">2010-05-11</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-08-09</td>
<td align="center">A2</td>
<td align="center">2010-05-17</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-12-29</td>
<td align="center">A2</td>
<td align="center">2010-05-18</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-02-03</td>
<td align="center">A2</td>
<td align="center">2010-07-30</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-15</td>
<td align="center">A2</td>
<td align="center">2010-09-15</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-22</td>
<td align="center">A2</td>
<td align="center">2010-10-06</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-06-10</td>
<td align="center">A2</td>
<td align="center">2010-11-30</td>
<td align="center">N3</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-20</td>
<td align="center">A2</td>
<td align="center">2011-01-27</td>
<td align="center">N3</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">FALSE</td>
@ -751,23 +751,23 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-08-06</td>
<td align="center">A2</td>
<td align="center">2011-01-30</td>
<td align="center">N3</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 8 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.4% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 1, now 7 isolates are flagged. In total, 78.7% of all isolates are marked ‘first weighted’ - 50.4% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</pre></body></html></div>
<p>So we end up with 15,719 isolates for analysis.</p>
<p>So we end up with 15,740 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">first</span>, <span class="no">keyab</span>))</pre></body></html></div>
@ -775,7 +775,6 @@ Longest: 1</p>
<div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">data_1st</span>)</pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -792,46 +791,13 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2014-09-10</td>
<td align="center">V9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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>3</td>
<td align="center">2014-05-27</td>
<td align="center">U4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>4</td>
<td align="center">2013-01-03</td>
<td align="center">I8</td>
<td align="center">Hospital B</td>
<td align="center">2014-04-15</td>
<td align="center">I4</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -840,51 +806,78 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2017-09-29</td>
<td align="center">T5</td>
<td align="center">2011-02-09</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-12-16</td>
<td align="center">K4</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">R</td>
<td align="center">S</td>
<td align="center">S</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="odd">
<td>8</td>
<td align="center">2012-07-08</td>
<td align="center">B2</td>
<tr class="even">
<td align="center">2017-08-23</td>
<td align="center">Z9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2014-01-07</td>
<td align="center">G7</td>
<tr class="odd">
<td align="center">2010-01-14</td>
<td align="center">N4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-01-31</td>
<td align="center">N1</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -906,8 +899,8 @@ Longest: 1</p>
<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>, <span class="no">species</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,719<br>
Available: 15,719 (100%, NA: 0 = 0%)<br>
Length: 15,740<br>
Available: 15,740 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -924,33 +917,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,906</td>
<td align="right">50.30%</td>
<td align="right">7,906</td>
<td align="right">50.30%</td>
<td align="right">7,938</td>
<td align="right">50.43%</td>
<td align="right">7,938</td>
<td align="right">50.43%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,898</td>
<td align="right">24.80%</td>
<td align="right">11,804</td>
<td align="right">75.09%</td>
<td align="right">3,883</td>
<td align="right">24.67%</td>
<td align="right">11,821</td>
<td align="right">75.10%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,330</td>
<td align="right">14.82%</td>
<td align="right">14,134</td>
<td align="right">89.92%</td>
<td align="right">2,317</td>
<td align="right">14.72%</td>
<td align="right">14,138</td>
<td align="right">89.82%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,585</td>
<td align="right">10.08%</td>
<td align="right">15,719</td>
<td align="right">1,602</td>
<td align="right">10.18%</td>
<td align="right">15,740</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -977,50 +970,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3784</td>
<td align="center">244</td>
<td align="center">3878</td>
<td align="center">7906</td>
<td align="center">3808</td>
<td align="center">236</td>
<td align="center">3894</td>
<td align="center">7938</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6252</td>
<td align="center">274</td>
<td align="center">1380</td>
<td align="center">7906</td>
<td align="center">6223</td>
<td align="center">317</td>
<td align="center">1398</td>
<td align="center">7938</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">6028</td>
<td align="center">6050</td>
<td align="center">0</td>
<td align="center">1878</td>
<td align="center">7906</td>
<td align="center">1888</td>
<td align="center">7938</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7176</td>
<td align="center">7130</td>
<td align="center">0</td>
<td align="center">730</td>
<td align="center">7906</td>
<td align="center">808</td>
<td align="center">7938</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1585</td>
<td align="center">1585</td>
<td align="center">1602</td>
<td align="center">1602</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1241</td>
<td align="center">60</td>
<td align="center">284</td>
<td align="center">1585</td>
<td align="center">61</td>
<td align="center">300</td>
<td align="center">1602</td>
</tr>
</tbody>
</table>
@ -1043,34 +1036,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">6028</td>
<td align="center">6050</td>
<td align="center">0</td>
<td align="center">1878</td>
<td align="center">7906</td>
<td align="center">1888</td>
<td align="center">7938</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1223</td>
<td align="center">1218</td>
<td align="center">0</td>
<td align="center">362</td>
<td align="center">1585</td>
<td align="center">384</td>
<td align="center">1602</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">2961</td>
<td align="center">2967</td>
<td align="center">0</td>
<td align="center">937</td>
<td align="center">3898</td>
<td align="center">916</td>
<td align="center">3883</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1777</td>
<td align="center">1756</td>
<td align="center">0</td>
<td align="center">553</td>
<td align="center">2330</td>
<td align="center">561</td>
<td align="center">2317</td>
</tr>
</tbody>
</table>
@ -1082,7 +1075,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>)
<span class="co"># [1] 0.5382022</span></pre></body></html></div>
<span class="co"># [1] 0.535324</span></pre></body></html></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital</span>) <span class="kw">%&gt;%</span>
@ -1096,19 +1089,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5410830</td>
<td align="center">0.5322921</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5318994</td>
<td align="center">0.5393839</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5342585</td>
<td align="center">0.5327529</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5477099</td>
<td align="center">0.5348690</td>
</tr>
</tbody>
</table>
@ -1127,23 +1120,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5410830</td>
<td align="center">4783</td>
<td align="center">0.5322921</td>
<td align="center">4738</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5318994</td>
<td align="center">5486</td>
<td align="center">0.5393839</td>
<td align="center">5421</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5342585</td>
<td align="center">2306</td>
<td align="center">0.5327529</td>
<td align="center">2412</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5477099</td>
<td align="center">3144</td>
<td align="center">0.5348690</td>
<td align="center">3169</td>
</tr>
</tbody>
</table>
@ -1164,27 +1157,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8254490</td>
<td align="center">0.9076651</td>
<td align="center">0.9864660</td>
<td align="center">0.8238851</td>
<td align="center">0.8982111</td>
<td align="center">0.9840010</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8208202</td>
<td align="center">0.9015773</td>
<td align="center">0.9892744</td>
<td align="center">0.8127341</td>
<td align="center">0.8951311</td>
<td align="center">0.9818976</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8134941</td>
<td align="center">0.9214982</td>
<td align="center">0.9858902</td>
<td align="center">0.8246201</td>
<td align="center">0.9260881</td>
<td align="center">0.9863508</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5454936</td>
<td align="center">0.5463962</td>
<td align="center">0.0000000</td>
<td align="center">0.5454936</td>
<td align="center">0.5463962</td>
</tr>
</tbody>
</table>

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

25
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>
@ -229,22 +229,23 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209010" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9010">
<a href="#amr-1209010" class="anchor"></a>AMR 1.2.0.9010<small> Unreleased </small>
<div id="amr-1209011" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9011">
<a href="#amr-1209011" class="anchor"></a>AMR 1.2.0.9011<small> Unreleased </small>
</h1>
<div id="last-updated-17-jun-2020" class="section level2">
<div id="last-updated-22-jun-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-17-jun-2020" class="anchor"></a><small>Last updated: 17-Jun-2020</small>
<a href="#last-updated-22-jun-2020" class="anchor"></a><small>Last updated: 22-Jun-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selections</a>, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selections</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
<span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span>())
<span class="co">#&gt; Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span>
@ -258,6 +259,10 @@
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">ab_class</a></span>(<span class="st">"mycobact"</span>))
<span class="co">#&gt; Selecting antimycobacterials: `RIF` (rifampicin)</span></pre></div>
</li>
<li><p>Added <code><a href="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><a href="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
<li><p>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</p></li>
<li><p>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code></p></li>
<li><p>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</p></li>
</ul>
</div>
<div id="changed" class="section level3">
@ -268,13 +273,11 @@
<li>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</li>
<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
<li>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>, and fixed a bug where not all different antimicrobial results were added as rows</li>
<li>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</li>
<li>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>
</li>
<li>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</li>
<li>Improved auto-determination for columns of types <code>&lt;mo&gt;</code> and <code>&lt;Date&gt;</code>
</li>
<li>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</li>
<li>Changed the summary for class <code>&lt;mo&gt;</code>, to highlight the %SI vs. %R</li>
<li>Improved error handling, giving more useful info when functions return an error</li>
</ul>
</div>
</div>

2
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-06-17T19:33Z
last_built: 2020-06-22T09:16Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

4
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>
@ -360,7 +360,7 @@
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

2
docs/reference/lifecycle.html
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@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>

17
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>
@ -257,6 +257,8 @@
<span class='fu'>mo_kingdom</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_domain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_type</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
@ -319,14 +321,15 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for <code>mo_ref()</code>, <code>mo_authors()</code> and <code>mo_year()</code>. This leads to the following results:</p><ul>
<li><p><code>mo_name("Chlamydia psittaci")</code> will return <code>"Chlamydophila psittaci"</code> (with a warning about the renaming)</p></li>
<li><p><code>mo_ref("Chlamydia psittaci")</code> will return <code>"Page, 1968"</code> (with a warning about the renaming)</p></li>
<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
<p>All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for <code>mo_ref()</code>, <code>mo_authors()</code> and <code>mo_year()</code>. Please refer to this example, knowing that <em>Escherichia blattae</em> was renamed to <em>Shimwellia blattae</em> in 2010:</p><ul>
<li><p><code>mo_name("Escherichia blattae")</code> will return <code>"Shimwellia blattae"</code> (with a message about the renaming)</p></li>
<li><p><code>mo_ref("Escherichia blattae")</code> will return <code>"Burgess et al., 1973"</code> (with a message about the renaming)</p></li>
<li><p><code>mo_ref("Shimwellia blattae")</code> will return <code>"Priest et al., 2010"</code> (without a message)</p></li>
</ul>
<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <em>"E. coli"</em>. Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like <em>"CoNS"</em> (Coagulase-Negative Staphylococci) and <em>"GBS"</em> (Group B Streptococci).</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (like <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href='as.mo.html'>as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

2
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@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
</span>
</div>