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dr. M.S. (Matthijs) Berends 2 years ago
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DESCRIPTION
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Package: AMR
Version: 1.0.0.9007
Version: 1.0.1
Date: 2020-02-22
Title: Antimicrobial Resistance Analysis
Authors@R: c(

7
NEWS.md
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@ -1,9 +1,8 @@ @@ -1,9 +1,8 @@
# AMR 1.0.0.9007
## <small>Last updated: 22-Feb-2020</small>
# AMR 1.0.1
### Changed
* Fixed floating point error for some MIC compa in EUCAST 2020 guideline
* Interpretation from MIC values to R/SI can now be used with `mutate_at()` of the dplyr package:
* Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
* Interpretation from MIC values (and disk zones) to R/SI can now be used with `mutate_at()` of the `dplyr` package:
```r
yourdata %>%
mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = "E. coli")

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docs/404.html
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@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</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">1.0.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>

2
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@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</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">1.0.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>

450
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@ -39,7 +39,7 @@ @@ -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">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>
@ -179,7 +179,7 @@ @@ -179,7 +179,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 February 2020</h4>
<h4 class="date">23 February 2020</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -188,7 +188,7 @@ @@ -188,7 +188,7 @@
<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 February 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 23 February 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -219,21 +219,21 @@ @@ -219,21 +219,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-02-20</td>
<td align="center">2020-02-23</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">2020-02-20</td>
<td align="center">2020-02-23</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">2020-02-20</td>
<td align="center">2020-02-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -328,10 +328,10 @@ @@ -328,10 +328,10 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-05</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2014-10-31</td>
<td align="center">B4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -339,59 +339,59 @@ @@ -339,59 +339,59 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-08-23</td>
<td align="center">J5</td>
<td align="center">2012-02-24</td>
<td align="center">E10</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">Escherichia 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">M</td>
</tr>
<tr class="odd">
<td align="center">2016-06-20</td>
<td align="center">S1</td>
<td align="center">2017-11-04</td>
<td align="center">G1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">M</td>
</tr>
<tr class="even">
<td align="center">2013-05-08</td>
<td align="center">J3</td>
<td align="center">Hospital A</td>
<td align="center">2011-10-08</td>
<td align="center">V4</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-12-28</td>
<td align="center">T8</td>
<td align="center">2016-02-16</td>
<td align="center">K6</td>
<td align="center">Hospital D</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">S</td>
<td align="center">F</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-11-05</td>
<td align="center">G9</td>
<td align="center">2014-05-28</td>
<td align="center">N6</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -423,16 +423,16 @@ Unique: 2</p> @@ -423,16 +423,16 @@ Unique: 2</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,402</td>
<td align="right">52.01%</td>
<td align="right">10,402</td>
<td align="right">52.01%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,598</td>
<td align="right">47.99%</td>
<td align="right">9,639</td>
<td align="right">48.20%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -447,65 +447,7 @@ Unique: 2</p> @@ -447,65 +447,7 @@ Unique: 2</p>
<span id="cb12-2"><a href="#cb12-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMX<span class="op">:</span>GEN), as.rsi)</span></code></pre></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"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a>data &lt;-<span class="st"> </span><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">col_mo =</span> <span class="st">"bacteria"</span>)</span>
<span id="cb13-2"><a href="#cb13-2"></a><span class="co"># </span></span>
<span id="cb13-3"><a href="#cb13-3"></a><span class="co"># Other rules by this AMR package</span></span>
<span id="cb13-4"><a href="#cb13-4"></a><span class="co"># Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)</span></span>
<span id="cb13-5"><a href="#cb13-5"></a><span class="co"># Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)</span></span>
<span id="cb13-6"><a href="#cb13-6"></a><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,986 values changed)</span></span>
<span id="cb13-7"><a href="#cb13-7"></a><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (157 values changed)</span></span>
<span id="cb13-8"><a href="#cb13-8"></a><span class="co"># Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)</span></span>
<span id="cb13-9"><a href="#cb13-9"></a><span class="co"># Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)</span></span>
<span id="cb13-10"><a href="#cb13-10"></a><span class="co"># Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></span>
<span id="cb13-11"><a href="#cb13-11"></a><span class="co"># Non-EUCAST: set trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></span>
<span id="cb13-12"><a href="#cb13-12"></a><span class="co"># </span></span>
<span id="cb13-13"><a href="#cb13-13"></a><span class="co"># ----</span></span>
<span id="cb13-14"><a href="#cb13-14"></a><span class="co"># Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</span></span>
<span id="cb13-15"><a href="#cb13-15"></a><span class="co"># http://eucast.org/</span></span>
<span id="cb13-16"><a href="#cb13-16"></a><span class="co"># </span></span>
<span id="cb13-17"><a href="#cb13-17"></a><span class="co"># EUCAST Clinical Breakpoints (v10.0, 2020)</span></span>
<span id="cb13-18"><a href="#cb13-18"></a><span class="co"># Aerococcus sanguinicola (no changes)</span></span>
<span id="cb13-19"><a href="#cb13-19"></a><span class="co"># Aerococcus urinae (no changes)</span></span>
<span id="cb13-20"><a href="#cb13-20"></a><span class="co"># Anaerobic Gram-negatives (no changes)</span></span>
<span id="cb13-21"><a href="#cb13-21"></a><span class="co"># Anaerobic Gram-positives (no changes)</span></span>
<span id="cb13-22"><a href="#cb13-22"></a><span class="co"># Burkholderia pseudomallei (no changes)</span></span>
<span id="cb13-23"><a href="#cb13-23"></a><span class="co"># Campylobacter coli (no changes)</span></span>
<span id="cb13-24"><a href="#cb13-24"></a><span class="co"># Campylobacter jejuni (no changes)</span></span>
<span id="cb13-25"><a href="#cb13-25"></a><span class="co"># Enterobacterales (Order) (no changes)</span></span>
<span id="cb13-26"><a href="#cb13-26"></a><span class="co"># Enterococcus (no changes)</span></span>
<span id="cb13-27"><a href="#cb13-27"></a><span class="co"># Haemophilus influenzae (no changes)</span></span>
<span id="cb13-28"><a href="#cb13-28"></a><span class="co"># Kingella kingae (no changes)</span></span>
<span id="cb13-29"><a href="#cb13-29"></a><span class="co"># Moraxella catarrhalis (no changes)</span></span>
<span id="cb13-30"><a href="#cb13-30"></a><span class="co"># Pasteurella multocida (no changes)</span></span>
<span id="cb13-31"><a href="#cb13-31"></a><span class="co"># Staphylococcus (no changes)</span></span>
<span id="cb13-32"><a href="#cb13-32"></a><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></span>
<span id="cb13-33"><a href="#cb13-33"></a><span class="co"># Streptococcus pneumoniae (1,017 values changed)</span></span>
<span id="cb13-34"><a href="#cb13-34"></a><span class="co"># Viridans group streptococci (no changes)</span></span>
<span id="cb13-35"><a href="#cb13-35"></a><span class="co"># </span></span>
<span id="cb13-36"><a href="#cb13-36"></a><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></span>
<span id="cb13-37"><a href="#cb13-37"></a><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,297 values changed)</span></span>
<span id="cb13-38"><a href="#cb13-38"></a><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></span>
<span id="cb13-39"><a href="#cb13-39"></a><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></span>
<span id="cb13-40"><a href="#cb13-40"></a><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,752 values changed)</span></span>
<span id="cb13-41"><a href="#cb13-41"></a><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></span>
<span id="cb13-42"><a href="#cb13-42"></a><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></span>
<span id="cb13-43"><a href="#cb13-43"></a><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></span>
<span id="cb13-44"><a href="#cb13-44"></a><span class="co"># Table 12: Interpretive rules for aminoglycosides (no changes)</span></span>
<span id="cb13-45"><a href="#cb13-45"></a><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></span>
<span id="cb13-46"><a href="#cb13-46"></a><span class="co"># </span></span>
<span id="cb13-47"><a href="#cb13-47"></a><span class="co"># -------------------------------------------------------------------------------</span></span>
<span id="cb13-48"><a href="#cb13-48"></a><span class="co"># EUCAST rules affected 6,502 out of 20,000 rows, making a total of 8,209 edits</span></span>
<span id="cb13-49"><a href="#cb13-49"></a><span class="co"># =&gt; added 0 test results</span></span>
<span id="cb13-50"><a href="#cb13-50"></a><span class="co"># </span></span>
<span id="cb13-51"><a href="#cb13-51"></a><span class="co"># =&gt; changed 8,209 test results</span></span>
<span id="cb13-52"><a href="#cb13-52"></a><span class="co"># - 124 test results changed from S to I</span></span>
<span id="cb13-53"><a href="#cb13-53"></a><span class="co"># - 4,743 test results changed from S to R</span></span>
<span id="cb13-54"><a href="#cb13-54"></a><span class="co"># - 1,209 test results changed from I to S</span></span>
<span id="cb13-55"><a href="#cb13-55"></a><span class="co"># - 356 test results changed from I to R</span></span>
<span id="cb13-56"><a href="#cb13-56"></a><span class="co"># - 1,777 test results changed from R to S</span></span>
<span id="cb13-57"><a href="#cb13-57"></a><span class="co"># -------------------------------------------------------------------------------</span></span>
<span id="cb13-58"><a href="#cb13-58"></a><span class="co"># </span></span>
<span id="cb13-59"><a href="#cb13-59"></a><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></span></code></pre></div>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a>data &lt;-<span class="st"> </span><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">col_mo =</span> <span class="st">"bacteria"</span>)</span></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -529,9 +471,8 @@ Unique: 2</p> @@ -529,9 +471,8 @@ Unique: 2</p>
<span id="cb15-2"><a href="#cb15-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">first =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(.))</span>
<span id="cb15-3"><a href="#cb15-3"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></span>
<span id="cb15-4"><a href="#cb15-4"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span>
<span id="cb15-5"><a href="#cb15-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span>
<span id="cb15-6"><a href="#cb15-6"></a><span class="co"># =&gt; Found 5,695 first isolates (28.5% of total)</span></span></code></pre></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 id="cb15-5"><a href="#cb15-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span></code></pre></div>
<p>So only 28.4% 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"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1"></a>data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb16-2"><a href="#cb16-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</span></code></pre></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>
@ -541,7 +482,7 @@ Unique: 2</p> @@ -541,7 +482,7 @@ Unique: 2</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 N2, 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 Q2, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -557,8 +498,8 @@ Unique: 2</p> @@ -557,8 +498,8 @@ Unique: 2</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-09</td>
<td align="center">N2</td>
<td align="center">2010-02-26</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -568,98 +509,98 @@ Unique: 2</p> @@ -568,98 +509,98 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-02</td>
<td align="center">N2</td>
<td align="center">2010-03-25</td>
<td align="center">Q2</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="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">N2</td>
<td align="center">2010-05-23</td>
<td align="center">Q2</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-19</td>
<td align="center">N2</td>
<td align="center">2010-05-24</td>
<td align="center">Q2</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>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-08</td>
<td align="center">N2</td>
<td align="center">2010-09-08</td>
<td align="center">Q2</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>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-09</td>
<td align="center">N2</td>
<td align="center">2011-03-19</td>
<td align="center">Q2</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-02</td>
<td align="center">Q2</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">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-05</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-06-19</td>
<td align="center">N2</td>
<td align="center">2011-11-13</td>
<td align="center">Q2</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-07-29</td>
<td align="center">N2</td>
<td align="center">2011-11-28</td>
<td align="center">Q2</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">S</td>
<td align="center">S</td>
@ -676,9 +617,7 @@ Unique: 2</p> @@ -676,9 +617,7 @@ Unique: 2</p>
<span id="cb18-5"><a href="#cb18-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></span>
<span id="cb18-6"><a href="#cb18-6"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span>
<span id="cb18-7"><a href="#cb18-7"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span>
<span id="cb18-8"><a href="#cb18-8"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></span>
<span id="cb18-9"><a href="#cb18-9"></a><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></span>
<span id="cb18-10"><a href="#cb18-10"></a><span class="co"># =&gt; Found 15,096 first weighted isolates (75.5% of total)</span></span></code></pre></div>
<span id="cb18-8"><a href="#cb18-8"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -695,8 +634,8 @@ Unique: 2</p> @@ -695,8 +634,8 @@ Unique: 2</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-09</td>
<td align="center">N2</td>
<td align="center">2010-02-26</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -707,23 +646,23 @@ Unique: 2</p> @@ -707,23 +646,23 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-02</td>
<td align="center">N2</td>
<td align="center">2010-03-25</td>
<td align="center">Q2</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">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">N2</td>
<td align="center">2010-05-23</td>
<td align="center">Q2</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -731,11 +670,11 @@ Unique: 2</p> @@ -731,11 +670,11 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-19</td>
<td align="center">N2</td>
<td align="center">2010-05-24</td>
<td align="center">Q2</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>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -743,83 +682,83 @@ Unique: 2</p> @@ -743,83 +682,83 @@ Unique: 2</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-08</td>
<td align="center">N2</td>
<td align="center">2010-09-08</td>
<td align="center">Q2</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>
<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">2010-08-09</td>
<td align="center">N2</td>
<td align="center">2011-03-19</td>
<td align="center">Q2</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-02</td>
<td align="center">Q2</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">TRUE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-05</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-06-19</td>
<td align="center">N2</td>
<td align="center">2011-11-13</td>
<td align="center">Q2</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-07-29</td>
<td align="center">N2</td>
<td align="center">2011-11-28</td>
<td align="center">Q2</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 9 isolates are flagged. In total, 75.5% of all isolates are marked ‘first weighted’ - 47.0% 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, 74.8% of all isolates are marked ‘first weighted’ - 46.4% 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"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a>data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb19-2"><a href="#cb19-2"></a><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</span></code></pre></div>
<p>So we end up with 15,096 isolates for analysis.</p>
<p>So we end up with 14,960 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a>data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb20-2"><a href="#cb20-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</span></code></pre></div>
@ -827,7 +766,6 @@ Unique: 2</p> @@ -827,7 +766,6 @@ Unique: 2</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(data_1st)</span></code></pre></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>
@ -844,30 +782,28 @@ Unique: 2</p> @@ -844,30 +782,28 @@ Unique: 2</p>
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2010-01-05</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2014-10-31</td>
<td align="center">B4</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2016-11-05</td>
<td align="center">G9</td>
<td align="center">Hospital C</td>
<td align="center">2012-02-24</td>
<td align="center">E10</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -876,14 +812,13 @@ Unique: 2</p> @@ -876,14 +812,13 @@ Unique: 2</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>7</td>
<td align="center">2016-05-20</td>
<td align="center">A10</td>
<td align="center">Hospital D</td>
<td align="center">2017-11-04</td>
<td align="center">G1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -892,10 +827,9 @@ Unique: 2</p> @@ -892,10 +827,9 @@ Unique: 2</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2015-10-02</td>
<td align="center">R3</td>
<td align="center">Hospital C</td>
<td align="center">2011-10-08</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -908,35 +842,33 @@ Unique: 2</p> @@ -908,35 +842,33 @@ Unique: 2</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>10</td>
<td align="center">2016-03-04</td>
<td align="center">B10</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">2016-02-16</td>
<td align="center">K6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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>11</td>
<td align="center">2013-09-10</td>
<td align="center">P4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">2014-05-28</td>
<td align="center">N6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -958,8 +890,8 @@ Unique: 2</p> @@ -958,8 +890,8 @@ Unique: 2</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus, species)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,096<br>
Available: 15,096 (100%, NA: 0 = 0%)<br>
Length: 14,960<br>
Available: 14,960 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -976,33 +908,33 @@ Longest: 24</p> @@ -976,33 +908,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,491</td>
<td align="right">49.62%</td>
<td align="right">7,491</td>
<td align="right">49.62%</td>
<td align="right">7,397</td>
<td align="right">49.45%</td>
<td align="right">7,397</td>
<td align="right">49.45%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,729</td>
<td align="right">24.70%</td>
<td align="right">11,220</td>
<td align="right">74.32%</td>
<td align="right">3,685</td>
<td align="right">24.63%</td>
<td align="right">11,082</td>
<td align="right">74.08%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,340</td>
<td align="right">15.50%</td>
<td align="right">13,560</td>
<td align="right">89.83%</td>
<td align="right">2,361</td>
<td align="right">15.78%</td>
<td align="right">13,443</td>
<td align="right">89.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,536</td>
<td align="right">10.17%</td>
<td align="right">15,096</td>
<td align="right">1,517</td>
<td align="right">10.14%</td>
<td align="right">14,960</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1014,7 +946,7 @@ Longest: 24</p> @@ -1014,7 +946,7 @@ 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"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX)</span>
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4681373</span></span></code></pre></div>
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4635695</span></span></code></pre></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"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb25-2"><a href="#cb25-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></span>
@ -1027,19 +959,19 @@ Longest: 24</p> @@ -1027,19 +959,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4648446</td>
<td align="center">0.4490022</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4689223</td>
<td align="center">0.4746786</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4656180</td>
<td align="center">0.4505104</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4734787</td>
<td align="center">0.4760039</td>
</tr>
</tbody>
</table>
@ -1057,23 +989,23 @@ Longest: 24</p> @@ -1057,23 +989,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4648446</td>
<td align="center">4537</td>
<td align="center">0.4490022</td>
<td align="center">4510</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4689223</td>
<td align="center">5261</td>
<td align="center">0.4746786</td>
<td align="center">5134</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4656180</td>
<td align="center">2225</td>
<td align="center">0.4505104</td>
<td align="center">2253</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4734787</td>
<td align="center">3073</td>
<td align="center">0.4760039</td>
<td align="center">3063</td>
</tr>
</tbody>
</table>
@ -1093,27 +1025,27 @@ Longest: 24</p> @@ -1093,27 +1025,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9255106</td>
<td align="center">0.8972100</td>
<td align="center">0.9937258</td>
<td align="center">0.9251048</td>
<td align="center">0.8952278</td>
<td align="center">0.9928349</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.9199219</td>
<td align="center">0.8932292</td>
<td align="center">0.9934896</td>
<td align="center">0.9169413</td>
<td align="center">0.9083718</td>
<td align="center">0.9947264</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9187450</td>
<td align="center">0.9133816</td>
<td align="center">0.9924913</td>
<td align="center">0.9305292</td>
<td align="center">0.9158752</td>
<td align="center">0.9937585</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6128205</td>
<td align="center">0.6027107</td>
<td align="center">0.0000000</td>
<td align="center">0.6128205</td>
<td align="center">0.6027107</td>
</tr>
</tbody>
</table>

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@ -39,7 +39,7 @@ @@ -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">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>
@ -179,7 +179,7 @@ @@ -179,7 +179,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 February 2020</h4>
<h4 class="date">23 February 2020</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

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@ -16,9 +16,7 @@ @@ -16,9 +16,7 @@
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