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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">1.1.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</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">20 May 2020</h4>
<h4 class="date">25 May 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 20 May 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 25 May 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">2020-05-20</td>
<td align="center">2020-05-25</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">2020-05-20</td>
<td align="center">2020-05-25</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">2020-05-20</td>
<td align="center">2020-05-25</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -336,41 +336,63 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-03-27</td>
<td align="center">L8</td>
<td align="center">2015-03-17</td>
<td align="center">U1</td>
<td align="center">Hospital D</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="even">
<td align="center">2017-08-02</td>
<td align="center">P6</td>
<td align="center">Hospital B</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="odd">
<td align="center">2017-06-24</td>
<td align="center">E4</td>
<td align="center">Hospital C</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="even">
<td align="center">2015-12-30</td>
<td align="center">K1</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2011-02-12</td>
<td align="center">I10</td>
<td align="center">Hospital D</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-06-06</td>
<td align="center">D3</td>
<td align="center">Hospital B</td>
<td align="center">2010-03-17</td>
<td align="center">Q3</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-07-04</td>
<td align="center">H10</td>
<td align="center">2010-08-19</td>
<td align="center">A7</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -379,28 +401,6 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-04-12</td>
<td align="center">M3</td>
<td align="center">Hospital B</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">2017-03-06</td>
<td align="center">S4</td>
<td align="center">Hospital C</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>
</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">10,403</td>
<td align="right">52.02%</td>
<td align="right">10,403</td>
<td align="right">52.02%</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">9,597</td>
<td align="right">47.99%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -456,11 +456,7 @@ Longest: 1</p>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">AMX</span>:<span class="no">GEN</span>), <span class="no">as.rsi</span>)</pre></body></html></div>
<p>Finally, we will apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p>Because the amoxicillin (column <code>AMX</code>) and amoxicillin/clavulanic acid (column <code>AMC</code>) in our data were generated randomly, some rows will undoubtedly contain AMX = S and AMC = R, which is technically impossible. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> fixes this:</p>
<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>, <span class="kw">col_mo</span> <span class="kw">=</span> <span class="st">"bacteria"</span>)
<span class="co"># [31m</span>
<span class="co"># Skipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.</span>
<span class="co"># Use eucast_rules(..., rules = "all") to also apply those rules.</span>
<span class="co"># [39m</span></pre></body></html></div>
<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>, <span class="kw">col_mo</span> <span class="kw">=</span> <span class="st">"bacteria"</span>)</pre></body></html></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -482,10 +478,10 @@ Longest: 1</p>
<p>This <code>AMR</code> package includes this methodology with the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function. It adopts the episode of a year (can be changed by user) and it starts counting days after every selected isolate. This new variable can easily be added to our data:</p>
<div class="sourceCode" id="cb15"><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">first</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">.</span>))
<span class="co"># [34mNOTE: Using column `[1mbacteria[22m` as input for `col_mo`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mdate[22m` as input for `col_date`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mpatient_id[22m` as input for `col_patient_id`.[39m</span></pre></body></html></div>
<p>So only 28.5% 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>
<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>
<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>
@ -495,7 +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 S1, 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 K4, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -511,32 +507,32 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-10</td>
<td align="center">S1</td>
<td align="center">2010-01-01</td>
<td align="center">K4</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-27</td>
<td align="center">S1</td>
<td align="center">2010-02-09</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">I</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">3</td>
<td align="center">2010-03-05</td>
<td align="center">S1</td>
<td align="center">2010-03-03</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</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>
@ -544,8 +540,8 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-04-03</td>
<td align="center">S1</td>
<td align="center">2010-04-25</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -555,19 +551,19 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-22</td>
<td align="center">S1</td>
<td align="center">2010-07-04</td>
<td align="center">K4</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-07-19</td>
<td align="center">S1</td>
<td align="center">2010-09-04</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">I</td>
@ -577,10 +573,10 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-07-19</td>
<td align="center">S1</td>
<td align="center">2010-10-01</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</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>
@ -588,30 +584,30 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-08-28</td>
<td align="center">S1</td>
<td align="center">2011-03-20</td>
<td align="center">K4</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">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-09</td>
<td align="center">S1</td>
<td align="center">2011-06-26</td>
<td align="center">K4</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-09-20</td>
<td align="center">S1</td>
<td align="center">2011-10-22</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -621,16 +617,16 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<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>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>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>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">first_weighted</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">.</span>))
<span class="co"># [34mNOTE: Using column `[1mbacteria[22m` as input for `col_mo`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mbacteria[22m` as input for `col_mo`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mdate[22m` as input for `col_date`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mpatient_id[22m` as input for `col_patient_id`.[39m</span>
<span class="co"># [34mNOTE: Using column `[1mkeyab[22m` as input for `col_keyantibiotics`. Use [1mcol_keyantibiotics = FALSE[22m to prevent this.[39m</span></pre></body></html></div>
<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
<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>
<span class="co"># NOTE: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -647,44 +643,44 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-10</td>
<td align="center">S1</td>
<td align="center">2010-01-01</td>
<td align="center">K4</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-27</td>
<td align="center">S1</td>
<td align="center">2010-02-09</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">I</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">3</td>
<td align="center">2010-03-05</td>
<td align="center">S1</td>
<td align="center">2010-03-03</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-04-03</td>
<td align="center">S1</td>
<td align="center">2010-04-25</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -695,34 +691,34 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-22</td>
<td align="center">S1</td>
<td align="center">2010-07-04</td>
<td align="center">K4</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">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="even">
<td align="center">6</td>
<td align="center">2010-07-19</td>
<td align="center">S1</td>
<td align="center">2010-09-04</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-07-19</td>
<td align="center">S1</td>
<td align="center">2010-10-01</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</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>
@ -731,32 +727,32 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-08-28</td>
<td align="center">S1</td>
<td align="center">2011-03-20</td>
<td align="center">K4</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">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-09</td>
<td align="center">S1</td>
<td align="center">2011-06-26</td>
<td align="center">K4</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-09-20</td>
<td align="center">S1</td>
<td align="center">2011-10-22</td>
<td align="center">K4</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -767,11 +763,11 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<p>Instead of 1, now 10 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 49.9% 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 2, now 7 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.1% 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 15,684 isolates for analysis.</p>
<p>So we end up with 15,673 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>
@ -797,14 +793,46 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2013-03-27</td>
<td align="center">L8</td>
<td align="center">2015-03-17</td>
<td align="center">U1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2017-08-02</td>
<td align="center">P6</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>4</td>
<td align="center">2011-02-12</td>
<td align="center">I10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
@ -812,41 +840,9 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2015-12-30</td>
<td align="center">K1</td>
<td align="center">Hospital B</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">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>3</td>
<td align="center">2016-06-06</td>
<td align="center">D3</td>
<td align="center">Hospital B</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>4</td>
<td align="center">2011-07-04</td>
<td align="center">H10</td>
<td>6</td>
<td align="center">2010-08-19</td>
<td align="center">A7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
@ -860,35 +856,35 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2017-03-06</td>
<td align="center">S4</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td>7</td>
<td align="center">2013-04-06</td>
<td align="center">H5</td>
<td align="center">Hospital A</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">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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2014-08-08</td>
<td align="center">C5</td>
<td>8</td>
<td align="center">2013-12-11</td>
<td align="center">J8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</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>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -910,8 +906,8 @@ 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: 15,684<br>
Available: 15,684 (100%, NA: 0 = 0%)<br>
Length: 15,673<br>
Available: 15,673 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -928,33 +924,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,819</td>
<td align="right">49.85%</td>
<td align="right">7,819</td>
<td align="right">49.85%</td>
<td align="right">7,843</td>
<td align="right">50.04%</td>
<td align="right">7,843</td>
<td align="right">50.04%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,992</td>
<td align="right">25.45%</td>
<td align="right">11,811</td>
<td align="right">75.31%</td>
<td align="right">3,949</td>
<td align="right">25.20%</td>
<td align="right">11,792</td>
<td align="right">75.24%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,332</td>
<td align="right">14.87%</td>
<td align="right">14,143</td>
<td align="right">90.17%</td>
<td align="right">2,320</td>
<td align="right">14.80%</td>
<td align="right">14,112</td>
<td align="right">90.04%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,541</td>
<td align="right">9.83%</td>
<td align="right">15,684</td>
<td align="right">1,561</td>
<td align="right">9.96%</td>
<td align="right">15,673</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -966,7 +962,7 @@ 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="cb24"><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] 0.4410227</span></pre></body></html></div>
<span class="co"># [1] 0.441396</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="cb25"><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>
@ -979,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4448217</td>
<td align="center">0.4339461</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4476345</td>
<td align="center">0.4463033</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4299828</td>
<td align="center">0.4511013</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4317450</td>
<td align="center">0.4368288</td>
</tr>
</tbody>
</table>
@ -1009,23 +1005,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4448217</td>
<td align="center">4712</td>
<td align="center">0.4339461</td>
<td align="center">4678</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4476345</td>
<td align="center">5538</td>
<td align="center">0.4463033</td>
<td align="center">5559</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4299828</td>
<td align="center">2328</td>
<td align="center">0.4511013</td>
<td align="center">2270</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4317450</td>
<td align="center">3106</td>
<td align="center">0.4368288</td>
<td align="center">3166</td>
</tr>
</tbody>
</table>
@ -1045,27 +1041,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8199258</td>
<td align="center">0.8988362</td>
<td align="center">0.9842691</td>
<td align="center">0.8236644</td>
<td align="center">0.8999107</td>
<td align="center">0.9832972</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8189487</td>
<td align="center">0.8916288</td>
<td align="center">0.9857236</td>
<td align="center">0.8315183</td>
<td align="center">0.8923767</td>
<td align="center">0.9820628</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8166333</td>
<td align="center">0.9170842</td>
<td align="center">0.9857214</td>
<td align="center">0.8219802</td>
<td align="center">0.9161813</td>
<td align="center">0.9853127</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6170669</td>
<td align="center">0.6224138</td>
<td align="center">0.0000000</td>
<td align="center">0.6170669</td>
<td align="center">0.6224138</td>
</tr>
</tbody>
</table>
@ -1141,8 +1137,7 @@ Longest: 24</p>
<a href="#independence-test" class="anchor"></a>Independence test</h2>
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis.</p>
<p>We will compare the resistance to fosfomycin (column <code>FOS</code>) in hospital A and D. The input for the <code><a href="https://rdrr.io/r/stats/fisher.test.html">fisher.test()</a></code> can be retrieved with a transformation like this:</p>
<div class="sourceCode" id="cb33"><html><body><pre class="r"><span class="co"># use package 'tidyr' to pivot data; </span>
<span class="co"># it gets installed with this 'AMR' package</span>
<div class="sourceCode" id="cb33"><html><body><pre class="r"><span class="co"># use package 'tidyr' to pivot data:</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">tidyr</span>)
<span class="no">check_FOS</span> <span class="kw">&lt;-</span> <span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
@ -1173,7 +1168,7 @@ Longest: 24</p>
<span class="co"># sample estimates:</span>
<span class="co"># odds ratio </span>
<span class="co"># 0.4488318</span></pre></body></html></div>
<p>As can be seen, the p value is 0.031, which means that the fosfomycin resistance found in hospital A and D are really different.</p>
<p>As can be seen, the p value is 0.031, which means that the fosfomycin resistance found in isolates from patients in hospital A and D are really different.</p>
</div>
</div>
</div>