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new EUCAST rules algorithm

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dr. M.S. (Matthijs) Berends
2019-04-05 18:47:39 +02:00
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docs/LICENSE-text.html
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@ -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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>

577
docs/articles/AMR.html
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@ -40,7 +40,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">27 March 2019</h4>
<h4 class="date">05 April 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -201,7 +201,7 @@
<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 27 March 2019.</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 05 April 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -217,21 +217,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-03-27</td>
<td align="center">2019-04-05</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">2019-03-27</td>
<td align="center">2019-04-05</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">2019-03-27</td>
<td align="center">2019-04-05</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,30 +327,19 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-10-28</td>
<td align="center">A4</td>
<td align="center">2015-03-05</td>
<td align="center">Z5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-07-22</td>
<td align="center">Y8</td>
<td align="center">Hospital C</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">2014-09-30</td>
<td align="center">N3</td>
<tr class="even">
<td align="center">2017-08-05</td>
<td align="center">K5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
@ -359,38 +348,49 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-08-31</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-02-14</td>
<td align="center">Z6</td>
<td align="center">2013-07-07</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-09-03</td>
<td align="center">O2</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-02-01</td>
<td align="center">D5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-12-28</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2014-03-20</td>
<td align="center">K9</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -411,8 +411,8 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,344 51.7% 10,344 51.7%
#&gt; 2 F 9,656 48.3% 20,000 100.0%</code></pre>
#&gt; 1 M 10,405 52.0% 10,405 52.0%
#&gt; 2 F 9,595 48.0% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -425,46 +425,59 @@
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">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>)</a>
<a class="sourceLine" id="cb14-2" title="2"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-3" title="3"><span class="co">#&gt; Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</span></a>
<a class="sourceLine" id="cb14-4" title="4"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-5" title="5"><span class="co">#&gt; EUCAST Clinical Breakpoints (v9.0, 2019)</span></a>
<a class="sourceLine" id="cb14-6" title="6"><span class="co">#&gt; Enterobacteriales (Order) (no changes)</span></a>
<a class="sourceLine" id="cb14-7" title="7"><span class="co">#&gt; Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-8" title="8"><span class="co">#&gt; Enterococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-9" title="9"><span class="co">#&gt; Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb14-10" title="10"><span class="co">#&gt; Streptococcus pneumoniae (no changes)</span></a>
<a class="sourceLine" id="cb14-11" title="11"><span class="co">#&gt; Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb14-12" title="12"><span class="co">#&gt; Haemophilus influenzae (no changes)</span></a>
<a class="sourceLine" id="cb14-13" title="13"><span class="co">#&gt; Moraxella catarrhalis (no changes)</span></a>
<a class="sourceLine" id="cb14-14" title="14"><span class="co">#&gt; Anaerobic Gram positives (no changes)</span></a>
<a class="sourceLine" id="cb14-15" title="15"><span class="co">#&gt; Anaerobic Gram negatives (no changes)</span></a>
<a class="sourceLine" id="cb14-16" title="16"><span class="co">#&gt; Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb14-17" title="17"><span class="co">#&gt; Campylobacter jejuni and C. coli (no changes)</span></a>
<a class="sourceLine" id="cb14-18" title="18"><span class="co">#&gt; Aerococcus sanguinicola and A. urinae (no changes)</span></a>
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#&gt; Kingella kingae (no changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#&gt; EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1342 changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#&gt; Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co">#&gt; Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2726 changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#&gt; Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co">#&gt; Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#&gt; Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-29" title="29"><span class="co">#&gt; Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
<a class="sourceLine" id="cb14-30" title="30"><span class="co">#&gt; Table 12: Interpretive rules for aminoglycosides (no changes)</span></a>
<a class="sourceLine" id="cb14-31" title="31"><span class="co">#&gt; Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb14-32" title="32"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-33" title="33"><span class="co">#&gt; Other rules</span></a>
<a class="sourceLine" id="cb14-34" title="34"><span class="co">#&gt; Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)</span></a>
<a class="sourceLine" id="cb14-35" title="35"><span class="co">#&gt; Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co">#&gt; Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co">#&gt; Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#&gt; Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#&gt; Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,400 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#&gt; -&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,068 test results (0 to S; 0 to I; 4,068 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-4" title="4"><span class="co">#&gt; http://eucast.org/</span></a>
<a class="sourceLine" id="cb14-5" title="5"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-6" title="6"><span class="co">#&gt; EUCAST Clinical Breakpoints (v9.0, 2019)</span></a>
<a class="sourceLine" id="cb14-7" title="7"><span class="co">#&gt; Aerococcus sanguinicola (no new changes)</span></a>
<a class="sourceLine" id="cb14-8" title="8"><span class="co">#&gt; Aerococcus urinae (no new changes)</span></a>
<a class="sourceLine" id="cb14-9" title="9"><span class="co">#&gt; Anaerobic Gram negatives (no new changes)</span></a>
<a class="sourceLine" id="cb14-10" title="10"><span class="co">#&gt; Anaerobic Gram positives (no new changes)</span></a>
<a class="sourceLine" id="cb14-11" title="11"><span class="co">#&gt; Campylobacter coli (no new changes)</span></a>
<a class="sourceLine" id="cb14-12" title="12"><span class="co">#&gt; Campylobacter jejuni (no new changes)</span></a>
<a class="sourceLine" id="cb14-13" title="13"><span class="co">#&gt; Enterobacteriales (Order) (no new changes)</span></a>
<a class="sourceLine" id="cb14-14" title="14"><span class="co">#&gt; Enterococcus (no new changes)</span></a>
<a class="sourceLine" id="cb14-15" title="15"><span class="co">#&gt; Haemophilus influenzae (no new changes)</span></a>
<a class="sourceLine" id="cb14-16" title="16"><span class="co">#&gt; Kingella kingae (no new changes)</span></a>
<a class="sourceLine" id="cb14-17" title="17"><span class="co">#&gt; Moraxella catarrhalis (no new changes)</span></a>
<a class="sourceLine" id="cb14-18" title="18"><span class="co">#&gt; Pasteurella multocida (no new changes)</span></a>
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#&gt; Staphylococcus (no new changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#&gt; Streptococcus groups A, B, C, G (no new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#&gt; Streptococcus pneumoniae (1476 new changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Viridans group streptococci (no new changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co">#&gt; EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 01: Intrinsic resistance in Enterobacteriaceae (1290 new changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#&gt; Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co">#&gt; Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#&gt; Table 04: Intrinsic resistance in Gram-positive bacteria (2758 new changes)</span></a>
<a class="sourceLine" id="cb14-29" title="29"><span class="co">#&gt; Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)</span></a>
<a class="sourceLine" id="cb14-30" title="30"><span class="co">#&gt; Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)</span></a>
<a class="sourceLine" id="cb14-31" title="31"><span class="co">#&gt; Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)</span></a>
<a class="sourceLine" id="cb14-32" title="32"><span class="co">#&gt; Table 12: Interpretive rules for aminoglycosides (no new changes)</span></a>
<a class="sourceLine" id="cb14-33" title="33"><span class="co">#&gt; Table 13: Interpretive rules for quinolones (no new changes)</span></a>
<a class="sourceLine" id="cb14-34" title="34"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-35" title="35"><span class="co">#&gt; Other rules</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co">#&gt; Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2311 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co">#&gt; Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (107 new changes)</span></a>
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#&gt; Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#&gt; Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#&gt; Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co">#&gt; EUCAST rules affected 6,584 out of 20,000 rows, making a total of 7,942 edits</span></a>
<a class="sourceLine" id="cb14-45" title="45"><span class="co">#&gt; =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-46" title="46"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co">#&gt; =&gt; changed 7,942 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co">#&gt; - 125 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co">#&gt; - 4,719 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co">#&gt; - 1,093 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co">#&gt; - 299 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co">#&gt; - 1,682 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co">#&gt; - 24 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-54" title="54"><span class="co">#&gt; --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-55" title="55"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-56" title="56"><span class="co">#&gt; Use verbose = TRUE to get a data.frame with all specified edits instead.</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -489,8 +502,8 @@
<a class="sourceLine" id="cb16-3" title="3"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" title="4"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" title="5"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,665 first isolates (28.3% of total)</span></a></code></pre></div>
<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>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,681 first isolates (28.4% of total)</span></a></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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" title="2"><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>)</a></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>
@ -516,87 +529,87 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-09-11</td>
<td align="center">L7</td>
<td align="center">2010-01-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-11-07</td>
<td align="center">L7</td>
<td align="center">2010-07-22</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">2011-01-16</td>
<td align="center">L7</td>
<td align="center">2010-07-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">2011-02-25</td>
<td align="center">L7</td>
<td align="center">2010-09-17</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="odd">
<td align="center">5</td>
<td align="center">2011-08-07</td>
<td align="center">L7</td>
<td align="center">2011-02-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">2011-08-16</td>
<td align="center">L7</td>
<td align="center">B_ESCHR_COL</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">7</td>
<td align="center">2011-10-08</td>
<td align="center">L7</td>
<td align="center">B_ESCHR_COL</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>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-10-26</td>
<td align="center">L7</td>
<td align="center">6</td>
<td align="center">2011-04-25</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="odd">
<td align="center">7</td>
<td align="center">2011-04-30</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">8</td>
<td align="center">2011-05-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -604,23 +617,23 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-01-15</td>
<td align="center">L7</td>
<td align="center">2011-06-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">10</td>
<td align="center">2012-02-08</td>
<td align="center">L7</td>
<td align="center">2011-10-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</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>
@ -637,7 +650,7 @@
<a class="sourceLine" id="cb19-7" title="7"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" title="8"><span class="co">#&gt; </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></a>
<a class="sourceLine" id="cb19-9" title="9"><span class="co">#&gt; [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,729 first weighted isolates (78.6% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,059 first weighted isolates (75.3% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,11 +667,11 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-09-11</td>
<td align="center">L7</td>
<td align="center">2010-01-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">TRUE</td>
@ -666,119 +679,119 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-11-07</td>
<td align="center">L7</td>
<td align="center">2010-07-22</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="odd">
<td align="center">3</td>
<td align="center">2011-01-16</td>
<td align="center">L7</td>
<td align="center">2010-07-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">2011-02-25</td>
<td align="center">L7</td>
<td align="center">2010-09-17</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-08-07</td>
<td align="center">L7</td>
<td align="center">2011-02-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-08-16</td>
<td align="center">L7</td>
<td align="center">2011-04-25</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-10-08</td>
<td align="center">L7</td>
<td align="center">2011-04-30</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-10-26</td>
<td align="center">L7</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">8</td>
<td align="center">2011-05-27</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-01-15</td>
<td align="center">L7</td>
<td align="center">2011-06-24</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">10</td>
<td align="center">2012-02-08</td>
<td align="center">L7</td>
<td align="center">2011-10-29</td>
<td align="center">N5</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</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>
</tbody>
</table>
<p>Instead of 2, now 10 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.3% 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 5 isolates are flagged. In total, 75.3% of all isolates are marked ‘first weighted’ - 46.9% 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>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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,729 isolates for analysis.</p>
<p>So we end up with 15,059 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" title="2"><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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -802,13 +815,58 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-10-28</td>
<td align="center">A4</td>
<td align="center">2015-03-05</td>
<td align="center">Z5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</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 align="center">2017-08-05</td>
<td align="center">K5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-08-31</td>
<td align="center">V4</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-07-07</td>
<td align="center">G5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</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 negative</td>
@ -816,44 +874,14 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-07-22</td>
<td align="center">Y8</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-09-30</td>
<td align="center">N3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-02-14</td>
<td align="center">Z6</td>
<td align="center">2015-09-03</td>
<td align="center">O2</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</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">Gram negative</td>
@ -861,34 +889,19 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-02-01</td>
<td align="center">D5</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-12-28</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td align="center">2014-03-20</td>
<td align="center">K9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -908,9 +921,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,729 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,059 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,729 (of which NA: 0 = 0.00%)<br>
Length: 15,059 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -927,33 +940,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,807</td>
<td align="right">49.6%</td>
<td align="right">7,807</td>
<td align="right">49.6%</td>
<td align="right">7,494</td>
<td align="right">49.8%</td>
<td align="right">7,494</td>
<td align="right">49.8%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,919</td>
<td align="right">24.9%</td>
<td align="right">11,726</td>
<td align="right">74.6%</td>
<td align="right">3,673</td>
<td align="right">24.4%</td>
<td align="right">11,167</td>
<td align="right">74.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,426</td>
<td align="right">2,325</td>
<td align="right">15.4%</td>
<td align="right">14,152</td>
<td align="right">90.0%</td>
<td align="right">13,492</td>
<td align="right">89.6%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,577</td>
<td align="right">10.0%</td>
<td align="right">15,729</td>
<td align="right">1,567</td>
<td align="right">10.4%</td>
<td align="right">15,059</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -964,7 +977,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_IR</a></span>(amox)</a>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4796236</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4999668</span></a></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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="2"><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></a>
@ -977,19 +990,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4841779</td>
<td align="center">0.5037963</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4800215</td>
<td align="center">0.5007457</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4663419</td>
<td align="center">0.5111524</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4815057</td>
<td align="center">0.4851550</td>
</tr>
</tbody>
</table>
@ -1007,23 +1020,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4841779</td>
<td align="center">4835</td>
<td align="center">0.5037963</td>
<td align="center">4478</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4800215</td>
<td align="center">5581</td>
<td align="center">0.5007457</td>
<td align="center">5364</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4663419</td>
<td align="center">2258</td>
<td align="center">0.5111524</td>
<td align="center">2152</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4815057</td>
<td align="center">3055</td>
<td align="center">0.4851550</td>
<td align="center">3065</td>
</tr>
</tbody>
</table>
@ -1043,27 +1056,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7376713</td>
<td align="center">0.8986807</td>
<td align="center">0.9754067</td>
<td align="center">0.8796370</td>
<td align="center">0.8973846</td>
<td align="center">0.9902589</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7305010</td>
<td align="center">0.8953710</td>
<td align="center">0.9727330</td>
<td align="center">0.7172942</td>
<td align="center">0.9081047</td>
<td align="center">0.9821315</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7305435</td>
<td align="center">0.9275325</td>
<td align="center">0.9793315</td>
<td align="center">0.8829295</td>
<td align="center">0.9221345</td>
<td align="center">0.9918323</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7320692</td>
<td align="center">0.5767742</td>
<td align="center">0.0000000</td>
<td align="center">0.7320692</td>
<td align="center">0.5767742</td>
</tr>
</tbody>
</table>

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@ -40,7 +40,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">27 March 2019</h4>
<h4 class="date">05 April 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>

203
docs/articles/benchmarks.html
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@ -40,7 +40,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">27 March 2019</h4>
<h4 class="date">05 April 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -218,13 +218,13 @@
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 18.0 18.0 22 18.0 20.0 48 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 48.0 48.0 76 67.0 92.0 150 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 18.0 18.0 24 19.0 22.0 62 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 18.0 18.0 23 18.0 20.0 61 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 29.0 29.0 35 29.0 30.0 76 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 29.0 29.0 37 29.0 30.0 79 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 8.2 8.2 13 8.2 8.4 52 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 18.0 18.0 27 18.0 20.0 62 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 48.0 48.0 61 49.0 91.0 92 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 18.0 18.0 18 18.0 18.0 19 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 18.0 18.0 18 18.0 18.0 20 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 29.0 29.0 29 29.0 29.0 29 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 28.0 29.0 48 29.0 73.0 130 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 8.1 8.1 13 8.2 8.6 52 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@ -236,12 +236,12 @@
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; as.mo("theisl") 460 460 500 510 510 560 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 460 470 490 490 510 530 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 74 74 84 75 78 120 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 74 75 88 75 120 120 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 73 73 84 74 75 130 10</span></a></code></pre></div>
<p>That takes 7.6 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; as.mo("theisl") 460 460 480 470 510 510 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 460 470 490 490 510 540 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 73 73 84 73 77 130 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 73 73 88 75 120 120 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 73 73 80 73 74 130 10</span></a></code></pre></div>
<p>That takes 8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
@ -257,111 +257,110 @@
<a class="sourceLine" id="cb4-12" title="12"> <span class="dt">main =</span> <span class="st">"Benchmarks per prevalence"</span>)</a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<p>In reality, the <code><a href="../reference/as.mo.html">as.mo()</a></code> functions <strong>learns from its own output to speed up determinations for next times</strong>. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use <code><a href="../reference/as.mo.html">as.mo()</a></code> yourself:</p>
<pre><code>#&gt; File /home/uscloud/.Rhistory_mo removed.</code></pre>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>The highest outliers are the first times. All next determinations were done in only thousands of seconds.</p>
<p>The highest outliers are the first times. All next determinations were done in only thousands of seconds. For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.</p>
<p>Still, uncommon microorganisms take a lot more time than common microorganisms, especially the first time. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_fullname()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb6-2" title="2"><span class="co"># take all MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb6-3" title="3">x &lt;-<span class="st"> </span>septic_patients<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-4" title="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a>
<a class="sourceLine" id="cb6-5" title="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-6" title="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="st"> </span><span class="co"># scramble it</span></a>
<a class="sourceLine" id="cb6-11" title="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a>
<a class="sourceLine" id="cb6-12" title="12"> </a>
<a class="sourceLine" id="cb6-13" title="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a>
<a class="sourceLine" id="cb6-14" title="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb6-15" title="15"><span class="co">#&gt; [1] 500000</span></a>
<a class="sourceLine" id="cb6-16" title="16"></a>
<a class="sourceLine" id="cb6-17" title="17"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb6-18" title="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb6-19" title="19"><span class="co">#&gt; [1] 50</span></a>
<a class="sourceLine" id="cb6-20" title="20"></a>
<a class="sourceLine" id="cb6-21" title="21"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb6-22" title="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
<a class="sourceLine" id="cb6-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-25" title="25"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-26" title="26"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-27" title="27"><span class="co">#&gt; mo_fullname(x) 825 845 887 867 903 1080 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.87 seconds (867 ms). You only lose time on your unique input values.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># take all MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb5-3" title="3">x &lt;-<span class="st"> </span>septic_patients<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-4" title="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a>
<a class="sourceLine" id="cb5-5" title="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-6" title="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a>
<a class="sourceLine" id="cb5-7" title="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-8" title="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a>
<a class="sourceLine" id="cb5-9" title="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-10" title="10"><span class="st"> </span><span class="co"># scramble it</span></a>
<a class="sourceLine" id="cb5-11" title="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a>
<a class="sourceLine" id="cb5-12" title="12"> </a>
<a class="sourceLine" id="cb5-13" title="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a>
<a class="sourceLine" id="cb5-14" title="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb5-15" title="15"><span class="co">#&gt; [1] 500000</span></a>
<a class="sourceLine" id="cb5-16" title="16"></a>
<a class="sourceLine" id="cb5-17" title="17"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb5-18" title="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb5-19" title="19"><span class="co">#&gt; [1] 50</span></a>
<a class="sourceLine" id="cb5-20" title="20"></a>
<a class="sourceLine" id="cb5-21" title="21"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb5-22" title="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
<a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" title="25"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#&gt; mo_fullname(x) 689 730 762 752 778 938 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.75 seconds (751 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_fullname()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb7-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb7-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-6" title="6"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-8" title="8"><span class="co">#&gt; A 12.400 12.700 13.100 13.000 13.400 13.700 10</span></a>
<a class="sourceLine" id="cb7-9" title="9"><span class="co">#&gt; B 26.300 26.600 27.900 28.400 28.700 29.000 10</span></a>
<a class="sourceLine" id="cb7-10" title="10"><span class="co">#&gt; C 0.486 0.502 0.727 0.821 0.849 0.982 10</span></a></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
<a class="sourceLine" id="cb6-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb6-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 12.200 12.300 12.500 12.400 12.600 13.40 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 25.800 26.300 26.800 26.600 26.900 28.50 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.477 0.724 0.779 0.825 0.848 1.07 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb8-4" title="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb8-5" title="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb8-6" title="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb8-7" title="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb8-8" title="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb8-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb8-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb8-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-13" title="13"><span class="co">#&gt; A 0.371 0.432 0.463 0.471 0.500 0.525 10</span></a>
<a class="sourceLine" id="cb8-14" title="14"><span class="co">#&gt; B 0.479 0.531 0.557 0.553 0.566 0.631 10</span></a>
<a class="sourceLine" id="cb8-15" title="15"><span class="co">#&gt; C 0.511 0.676 0.834 0.904 0.959 1.090 10</span></a>
<a class="sourceLine" id="cb8-16" title="16"><span class="co">#&gt; D 0.422 0.444 0.483 0.494 0.501 0.559 10</span></a>
<a class="sourceLine" id="cb8-17" title="17"><span class="co">#&gt; E 0.383 0.458 0.502 0.477 0.507 0.778 10</span></a>
<a class="sourceLine" id="cb8-18" title="18"><span class="co">#&gt; F 0.362 0.376 0.476 0.426 0.473 0.947 10</span></a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; G 0.361 0.368 0.451 0.452 0.500 0.610 10</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; H 0.359 0.383 0.431 0.437 0.458 0.505 10</span></a></code></pre></div>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb7-4" title="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb7-5" title="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb7-6" title="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb7-7" title="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb7-8" title="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb7-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.376 0.386 0.436 0.436 0.479 0.516 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.467 0.501 0.561 0.567 0.599 0.700 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.503 0.782 0.850 0.918 0.971 1.040 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.403 0.471 0.488 0.491 0.525 0.588 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.343 0.429 0.456 0.445 0.485 0.638 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.380 0.403 0.447 0.453 0.491 0.520 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.385 0.421 0.458 0.447 0.487 0.575 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.396 0.455 0.484 0.491 0.515 0.549 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
<h3 class="hasAnchor">
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_fullname("CoNS") on an English system</span></a>
<a class="sourceLine" id="cb9-2" title="2"><span class="co">#&gt; [1] "Coagulase-negative Staphylococcus (CoNS)"</span></a>
<a class="sourceLine" id="cb9-3" title="3"></a>
<a class="sourceLine" id="cb9-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_fullname("CoNS") on a Spanish system</span></a>
<a class="sourceLine" id="cb9-5" title="5"><span class="co">#&gt; [1] "Staphylococcus coagulasa negativo (SCN)"</span></a>
<a class="sourceLine" id="cb9-6" title="6"></a>
<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_fullname("CoNS") on a Dutch system</span></a>
<a class="sourceLine" id="cb9-8" title="8"><span class="co">#&gt; [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a>
<a class="sourceLine" id="cb9-9" title="9"></a>
<a class="sourceLine" id="cb9-10" title="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb9-11" title="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb9-12" title="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb9-13" title="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb9-14" title="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb9-15" title="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb9-16" title="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb9-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb9-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb9-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb9-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb9-21" title="21"><span class="co">#&gt; en 18.83 19.19 24.20 19.53 20.67 63.66 10</span></a>
<a class="sourceLine" id="cb9-22" title="22"><span class="co">#&gt; de 31.53 32.10 36.79 32.22 33.81 75.80 10</span></a>
<a class="sourceLine" id="cb9-23" title="23"><span class="co">#&gt; nl 31.24 31.78 32.22 32.10 32.24 33.43 10</span></a>
<a class="sourceLine" id="cb9-24" title="24"><span class="co">#&gt; es 31.40 32.07 45.82 33.08 75.31 76.95 10</span></a>
<a class="sourceLine" id="cb9-25" title="25"><span class="co">#&gt; it 31.17 31.95 36.82 32.09 32.19 79.48 10</span></a>
<a class="sourceLine" id="cb9-26" title="26"><span class="co">#&gt; fr 31.48 31.64 31.89 31.96 32.07 32.33 10</span></a>
<a class="sourceLine" id="cb9-27" title="27"><span class="co">#&gt; pt 31.27 31.66 36.80 32.06 32.34 80.53 10</span></a></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_fullname("CoNS") on an English system</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="co">#&gt; [1] "Coagulase-negative Staphylococcus (CoNS)"</span></a>
<a class="sourceLine" id="cb8-3" title="3"></a>
<a class="sourceLine" id="cb8-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_fullname("CoNS") on a Spanish system</span></a>
<a class="sourceLine" id="cb8-5" title="5"><span class="co">#&gt; [1] "Staphylococcus coagulasa negativo (SCN)"</span></a>
<a class="sourceLine" id="cb8-6" title="6"></a>
<a class="sourceLine" id="cb8-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_fullname("CoNS") on a Dutch system</span></a>
<a class="sourceLine" id="cb8-8" title="8"><span class="co">#&gt; [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a>
<a class="sourceLine" id="cb8-9" title="9"></a>
<a class="sourceLine" id="cb8-10" title="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb8-11" title="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb8-12" title="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb8-13" title="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb8-14" title="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb8-15" title="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb8-16" title="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb8-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 18.96 19.05 19.17 19.10 19.28 19.50 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 31.11 31.58 40.75 32.11 33.36 75.57 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 31.18 31.55 39.10 31.77 32.52 75.92 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 30.76 31.46 40.46 31.62 33.07 75.85 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 31.02 31.41 36.06 31.67 31.95 76.19 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 31.02 31.66 36.36 31.84 32.46 76.22 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 31.13 31.58 31.78 31.65 31.74 33.00 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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@ -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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>

2
docs/authors.html
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@ -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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>

4
docs/index.html
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@ -42,7 +42,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -281,7 +281,7 @@
<p>The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p>
</li>
<li><p>All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>This data is updated annually - check the included version with <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>

61
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@ -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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -232,9 +232,40 @@
</div>
<div id="amr-0619001" class="section level1">
<h1 class="page-header">
<a href="#amr-0619001" class="anchor"></a>AMR 0.6.1.9001<small> Unreleased </small>
</h1>
<p><strong>Note: latest development version</strong></p>
<div id="changed" class="section level4">
<h4 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h4>
<ul>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>
</li>
<li>Added more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><a href="../reference/as.mo.html">as.mo()</a></code> function</li>
<li>Frequency tables of microbial IDs speed improvement</li>
<li>Removed all hardcoded EUCAST rules and replaced them with a new reference file: <code>./inst/eucast/eucast.tsv</code>.</li>
</ul>
</div>
</div>
<div id="amr-061" class="section level1">
<h1 class="page-header">
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
</h1>
<div id="changed-1" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
</li>
<li>Coercion of microbial IDs are now written to the package namespace instead of the user’s home folder, to comply with the CRAN policy</li>
</ul>
</div>
</div>
<div id="amr-060" class="section level1">
<h1 class="page-header">
<a href="#amr-060" class="anchor"></a>AMR 0.6.0<small> Unreleased </small>
<a href="#amr-060" class="anchor"></a>AMR 0.6.0<small> 2019-03-27 </small>
</h1>
<p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p>
@ -328,9 +359,9 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul>
</div>
<div id="changed" class="section level4">
<div id="changed-2" class="section level4">
<h4 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h4>
<a href="#changed-2" class="anchor"></a>Changed</h4>
<ul>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
@ -344,8 +375,8 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
<li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
<li>Functions <code><a href="../reference/AMR-deprecated.html">atc_ddd()</a></code> and <code><a href="../reference/AMR-deprecated.html">atc_groups()</a></code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_atc()</a></code> is now deprecated in favour of <code><a href="../reference/as.atc.html">as.atc()</a></code> and will be removed in future versions</li>
<li>Function <code>guess_mo()</code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Function <code>guess_atc()</code> is now deprecated in favour of <code><a href="../reference/as.atc.html">as.atc()</a></code> and will be removed in future versions</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>
@ -483,9 +514,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
</ul>
</div>
<div id="changed-1" class="section level4">
<div id="changed-3" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h4>
<a href="#changed-3" class="anchor"></a>Changed</h4>
<ul>
<li>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code>
</li>
@ -667,9 +698,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
</ul>
</div>
<div id="changed-2" class="section level4">
<div id="changed-4" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-2" class="anchor"></a>Changed</h4>
<a href="#changed-4" class="anchor"></a>Changed</h4>
<ul>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>
@ -804,9 +835,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
</ul>
</div>
<div id="changed-3" class="section level4">
<div id="changed-5" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-3" class="anchor"></a>Changed</h4>
<a href="#changed-5" class="anchor"></a>Changed</h4>
<ul>
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
<li>More antibiotics added as parameters for EUCAST rules</li>
@ -890,9 +921,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
</ul>
</div>
<div id="changed-4" class="section level4">
<div id="changed-6" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-4" class="anchor"></a>Changed</h4>
<a href="#changed-6" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
@ -949,6 +980,8 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0619001">0.6.1.9001</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>
<li><a href="#amr-050">0.5.0</a></li>
<li><a href="#amr-040">0.4.0</a></li>

6
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@ -80,7 +80,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -243,10 +243,6 @@
<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)
<span class='fu'>guess_mo</span>(<span class='no'>...</span>)
<span class='fu'>guess_atc</span>(<span class='no'>...</span>)
<span class='fu'>ab_property</span>(<span class='no'>...</span>)
<span class='fu'>ab_atc</span>(<span class='no'>...</span>)

6
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@ -80,7 +80,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -311,7 +311,9 @@ A microbial ID from this package (class: <code>mo</code>) typically looks like t
<p>Use the <code><a href='mo_property.html'>mo_property</a>_*</code> functions to get properties based on the returned code, see Examples.</p>
<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <code><a href='microorganisms.html'>?microorganisms</a></code>).</p>
<p><strong>Self-learning algoritm</strong> <br />
The <code>as.mo()</code> function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use <code>clean_mo_history()</code> to reset the algorithms. Only experience from your current <code>AMR</code> package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge. Usually, any guess after the first try runs 80-95% faster than the first try. The algorithm saves its previous findings to <code>~/.Rhistory_mo</code>.</p>
The <code>as.mo()</code> function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use <code>clean_mo_history()</code> to reset the algorithms. Only experience from your current <code>AMR</code> package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge.</p>
<p>Usually, any guess after the first try runs 80-95% faster than the first try.</p>
<p>For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.</p>
<p><strong>Intelligent rules</strong> <br />
This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:</p><ul>
<li><p>Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations</p></li>

4
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@ -80,7 +80,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -256,7 +256,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa</p></li>
<li><p>All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

10
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -345,15 +345,15 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1057 (67.1%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1576</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1342 (71.4%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1879</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># S = 1372 (74.0%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># n = 1855</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1396 (92.0%)</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1517</span>
<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1660 (92.3%)</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1798</span>
<span class='fu'>n_rsi</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>))
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>

89
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@ -80,7 +80,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -241,51 +241,48 @@
</div>
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>azlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mezl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>oxac</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>pris</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>())
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>,
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>azlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>mezl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>oxac</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pris</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
<span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='no'>...</span>)
<span class='fu'>EUCAST_rules</span>(<span class='no'>...</span>)
<span class='fu'>interpretive_reading</span>(<span class='no'>...</span>)</pre>
<span class='fu'>eucast_rules_file</span>()</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tbl</th>
<td><p>table with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td>
<th>x</th>
<td><p>data with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td>
</tr>
<tr>
<th>col_mo</th>
@ -324,10 +321,18 @@
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
</ul>
<p>For editing the reference file (which is available with <code>eucast_rules_file</code>), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: <code>"amcl, fluoroquinolones"</code>. The mo_property can be any column name from the <code><a href='microorganisms.html'>microorganisms</a></code> data set, or <code>genus_species</code> or <code>gramstain</code>. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with all original and new values of the affected bug-drug combinations.</p>
<p>The input of <code>tbl_</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with all original and new values of the affected bug-drug combinations.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The file used for applying all EUCAST rules can be retrieved with <code>eucast_rules_file()</code>. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: <br />
<code>AMR::EUCAST_RULES_FILE_LOCATION</code> (without brackets).</p>
<p>In the source code it is located under <a href='https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv'><code>./inst/eucast/eucast_rules.tsv</code></a>.</p>
<p><strong>Note:</strong> When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -456,6 +461,8 @@
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>

6
docs/reference/index.html
View File

@ -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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -311,7 +311,7 @@
</tr><tr>
<td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">EUCAST_rules()</a></code> <code><a href="eucast_rules.html">interpretive_reading()</a></code> </p>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_rules_file()</a></code> </p>
</td>
<td><p>EUCAST rules</p></td>
</tr><tr>
@ -549,7 +549,7 @@
<tr>
<td>
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">guess_mo()</a></code> <code><a href="AMR-deprecated.html">guess_atc()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> <code><a href="AMR-deprecated.html">atc_ddd()</a></code> <code><a href="AMR-deprecated.html">atc_groups()</a></code> </p>
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> <code><a href="AMR-deprecated.html">atc_ddd()</a></code> <code><a href="AMR-deprecated.html">atc_groups()</a></code> </p>
</td>
<td><p>Deprecated functions</p></td>
</tr>

12
docs/reference/microorganisms.old.html
View File

@ -80,7 +80,7 @@
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -245,16 +245,16 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 16,911 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>tsn_new</code></dt><dd><p>New Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Old taxonomic name of the microorganism</p></dd>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 21,342 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID that was originally given</p></dd>
<dt><code>col_id_new</code></dt><dd><p>New Catalogue of Life ID that responds to an entry in the <code><a href='microorganisms.html'>microorganisms</a></code> data set</p></dd>
<dt><code>fullname</code></dt><dd><p>Old full taxonomic name of the microorganism</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>[3] Catalogue of Life: Annual Checklist (public online database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a>.</p>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>

10
docs/reference/portion.html
View File

@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</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="Released version">0.6.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
</span>
</div>
@ -368,14 +368,14 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>) <span class='co'># S = 67.1%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>) <span class='co'># n = 1576</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>) <span class='co'># S = 71.4%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>) <span class='co'># n = 1879</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>) <span class='co'># S = 74.0%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>) <span class='co'># n = 1855</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># S = 92.0%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># n = 1517</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># S = 92.3%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># n = 1798</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>