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@ -192,7 +192,7 @@
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<h1>How to conduct AMR analysis</h1>
|
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">21 February 2019</h4>
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<h4 class="date">22 February 2019</h4>
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<div class="hidden name"><code>AMR.Rmd</code></div>
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@ -201,7 +201,7 @@
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<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/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 21 February 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/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 22 February 2019.</p>
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<div id="introduction" class="section level1">
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<h1 class="hasAnchor">
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<a href="#introduction" class="anchor"></a>Introduction</h1>
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@ -217,21 +217,21 @@
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||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2019-02-21</td>
|
||||
<td align="center">2019-02-22</td>
|
||||
<td align="center">abcd</td>
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||||
<td align="center">Escherichia coli</td>
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||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2019-02-21</td>
|
||||
<td align="center">2019-02-22</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2019-02-21</td>
|
||||
<td align="center">2019-02-22</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -327,65 +327,65 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-03-19</td>
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||||
<td align="center">Z1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2014-11-25</td>
|
||||
<td align="center">O2</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-12-24</td>
|
||||
<td align="center">Z8</td>
|
||||
<td align="center">Hospital A</td>
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||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">2016-11-18</td>
|
||||
<td align="center">I10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2013-12-12</td>
|
||||
<td align="center">Z1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2014-08-15</td>
|
||||
<td align="center">G9</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-07-26</td>
|
||||
<td align="center">S2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-08-13</td>
|
||||
<td align="center">J4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-04-09</td>
|
||||
<td align="center">F5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2017-01-25</td>
|
||||
<td align="center">H5</td>
|
||||
<td align="center">Hospital C</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">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-08-11</td>
|
||||
<td align="center">N1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">2017-03-12</td>
|
||||
<td align="center">B9</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -411,8 +411,8 @@
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||||
#>
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||||
#> Item Count Percent Cum. Count Cum. Percent
|
||||
#> --- ----- ------- -------- ----------- -------------
|
||||
#> 1 M 10,436 52.2% 10,436 52.2%
|
||||
#> 2 F 9,564 47.8% 20,000 100.0%</code></pre>
|
||||
#> 1 M 10,377 51.9% 10,377 51.9%
|
||||
#> 2 F 9,623 48.1% 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 <-<span class="st"> </span>data <span class="op">%>%</span></a>
|
||||
@ -443,10 +443,10 @@
|
||||
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#> Kingella kingae (no changes)</span></a>
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||||
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#> </span></a>
|
||||
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
|
||||
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#> Table 1: Intrinsic resistance in Enterobacteriaceae (1333 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#> Table 1: Intrinsic resistance in Enterobacteriaceae (1284 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#> 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">#> Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#> Table 4: Intrinsic resistance in Gram-positive bacteria (2733 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#> Table 4: Intrinsic resistance in Gram-positive bacteria (2790 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#> 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">#> 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">#> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
|
||||
@ -462,9 +462,9 @@
|
||||
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#> </span></a>
|
||||
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#> => EUCAST rules affected 7,452 out of 20,000 rows</span></a>
|
||||
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#> => EUCAST rules affected 7,321 out of 20,000 rows</span></a>
|
||||
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#> -> added 0 test results</span></a>
|
||||
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#> -> changed 4,066 test results (0 to S; 0 to I; 4,066 to R)</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#> -> changed 4,074 test results (0 to S; 0 to I; 4,074 to R)</span></a></code></pre></div>
|
||||
</div>
|
||||
<div id="adding-new-variables" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
@ -489,8 +489,8 @@
|
||||
<a class="sourceLine" id="cb16-3" title="3"><span class="co">#> </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">#> </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">#> </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">#> => Found 5,692 first isolates (28.5% of total)</span></a></code></pre></div>
|
||||
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#> => Found 5,680 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 <-<span class="st"> </span>data <span class="op">%>%</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>
|
||||
@ -516,32 +516,32 @@
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-14</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-01-10</td>
|
||||
<td align="center">X9</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</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">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-02-22</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-04-18</td>
|
||||
<td align="center">X9</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">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-04-01</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-07-02</td>
|
||||
<td align="center">X9</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>
|
||||
@ -549,21 +549,21 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-04-25</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-09-21</td>
|
||||
<td align="center">X9</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>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-05-09</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-09-22</td>
|
||||
<td align="center">X9</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>
|
||||
@ -571,21 +571,21 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-05-29</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-10-06</td>
|
||||
<td align="center">X9</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="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2010-06-27</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-10-14</td>
|
||||
<td align="center">X9</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>
|
||||
@ -593,19 +593,19 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2010-06-27</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2011-01-09</td>
|
||||
<td align="center">X9</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">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-02-01</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2011-03-31</td>
|
||||
<td align="center">X9</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -615,12 +615,12 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-03-20</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2011-03-31</td>
|
||||
<td align="center">X9</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>
|
||||
@ -637,7 +637,7 @@
|
||||
<a class="sourceLine" id="cb19-7" title="7"><span class="co">#> </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">#> </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">#> [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
|
||||
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#> => Found 15,851 first weighted isolates (79.3% of total)</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#> => Found 15,854 first weighted isolates (79.3% of total)</span></a></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">isolate</th>
|
||||
@ -654,34 +654,34 @@
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-14</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-01-10</td>
|
||||
<td align="center">X9</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</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">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-02-22</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-04-18</td>
|
||||
<td align="center">X9</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">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">3</td>
|
||||
<td align="center">2010-04-01</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-07-02</td>
|
||||
<td align="center">X9</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>
|
||||
@ -690,44 +690,32 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-04-25</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2010-09-21</td>
|
||||
<td align="center">X9</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>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-05-09</td>
|
||||
<td align="center">O6</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="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-05-29</td>
|
||||
<td align="center">O6</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">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2010-06-27</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-09-22</td>
|
||||
<td align="center">X9</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-10-06</td>
|
||||
<td align="center">X9</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -736,22 +724,34 @@
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2010-10-14</td>
|
||||
<td align="center">X9</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2010-06-27</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2011-01-09</td>
|
||||
<td align="center">X9</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">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-02-01</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2011-03-31</td>
|
||||
<td align="center">X9</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -762,23 +762,23 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-03-20</td>
|
||||
<td align="center">O6</td>
|
||||
<td align="center">2011-03-31</td>
|
||||
<td align="center">X9</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">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Instead of 2, now 6 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 50.8% 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 8 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 50.9% 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 <-<span class="st"> </span>data <span class="op">%>%</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 15,851 isolates for analysis.</p>
|
||||
<p>So we end up with 15,854 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 <-<span class="st"> </span>data_1st <span class="op">%>%</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>
|
||||
@ -803,10 +803,58 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>3</td>
|
||||
<td align="center">2013-12-12</td>
|
||||
<td align="center">Z1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td>2</td>
|
||||
<td align="center">2016-11-18</td>
|
||||
<td align="center">I10</td>
|
||||
<td align="center">Hospital B</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>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>5</td>
|
||||
<td align="center">2017-01-25</td>
|
||||
<td align="center">H5</td>
|
||||
<td align="center">Hospital C</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">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>6</td>
|
||||
<td align="center">2017-03-12</td>
|
||||
<td align="center">B9</td>
|
||||
<td align="center">Hospital C</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">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>7</td>
|
||||
<td align="center">2015-08-12</td>
|
||||
<td align="center">Y4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AUR</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -818,26 +866,10 @@
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>4</td>
|
||||
<td align="center">2014-08-13</td>
|
||||
<td align="center">J4</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">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>5</td>
|
||||
<td align="center">2012-04-09</td>
|
||||
<td align="center">F5</td>
|
||||
<td>9</td>
|
||||
<td align="center">2016-01-24</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
@ -851,44 +883,12 @@
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>6</td>
|
||||
<td align="center">2010-08-11</td>
|
||||
<td align="center">N1</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">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>7</td>
|
||||
<td align="center">2010-02-25</td>
|
||||
<td align="center">E9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_KLBSL_PNE</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>8</td>
|
||||
<td align="center">2013-04-09</td>
|
||||
<td align="center">N1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td>12</td>
|
||||
<td align="center">2013-09-11</td>
|
||||
<td align="center">H6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AUR</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -915,9 +915,9 @@
|
||||
<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">%>%</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> (15,851 x 13)</strong></p>
|
||||
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,854 x 13)</strong></p>
|
||||
<p>Columns: 2<br>
|
||||
Length: 15,851 (of which NA: 0 = 0.00%)<br>
|
||||
Length: 15,854 (of which NA: 0 = 0.00%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -934,33 +934,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">7,853</td>
|
||||
<td align="right">49.5%</td>
|
||||
<td align="right">7,853</td>
|
||||
<td align="right">49.5%</td>
|
||||
<td align="right">7,918</td>
|
||||
<td align="right">49.9%</td>
|
||||
<td align="right">7,918</td>
|
||||
<td align="right">49.9%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">3,943</td>
|
||||
<td align="right">24.9%</td>
|
||||
<td align="right">11,796</td>
|
||||
<td align="right">74.4%</td>
|
||||
<td align="right">3,930</td>
|
||||
<td align="right">24.8%</td>
|
||||
<td align="right">11,848</td>
|
||||
<td align="right">74.7%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,432</td>
|
||||
<td align="right">15.3%</td>
|
||||
<td align="right">14,228</td>
|
||||
<td align="right">89.8%</td>
|
||||
<td align="right">2,498</td>
|
||||
<td align="right">15.8%</td>
|
||||
<td align="right">14,346</td>
|
||||
<td align="right">90.5%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,623</td>
|
||||
<td align="right">10.2%</td>
|
||||
<td align="right">15,851</td>
|
||||
<td align="right">1,508</td>
|
||||
<td align="right">9.5%</td>
|
||||
<td align="right">15,854</td>
|
||||
<td align="right">100.0%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -971,7 +971,7 @@ Longest: 24</p>
|
||||
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
|
||||
<p>The functions <code>portion_R</code>, <code>portion_RI</code>, <code>portion_I</code>, <code>portion_IS</code> and <code>portion_S</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">%>%</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">#> [1] 0.4764368</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#> [1] 0.4726883</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">%>%</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">%>%</span><span class="st"> </span></a>
|
||||
@ -984,19 +984,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4722165</td>
|
||||
<td align="center">0.4737395</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4788707</td>
|
||||
<td align="center">0.4763709</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4670535</td>
|
||||
<td align="center">0.4739257</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4859994</td>
|
||||
<td align="center">0.4636854</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1014,23 +1014,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4722165</td>
|
||||
<td align="center">4841</td>
|
||||
<td align="center">0.4737395</td>
|
||||
<td align="center">4760</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4788707</td>
|
||||
<td align="center">5490</td>
|
||||
<td align="center">0.4763709</td>
|
||||
<td align="center">5544</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4670535</td>
|
||||
<td align="center">2413</td>
|
||||
<td align="center">0.4739257</td>
|
||||
<td align="center">2397</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4859994</td>
|
||||
<td align="center">3107</td>
|
||||
<td align="center">0.4636854</td>
|
||||
<td align="center">3153</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1050,27 +1050,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7324589</td>
|
||||
<td align="center">0.9016936</td>
|
||||
<td align="center">0.9759328</td>
|
||||
<td align="center">0.7350341</td>
|
||||
<td align="center">0.9051528</td>
|
||||
<td align="center">0.9761303</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.7221195</td>
|
||||
<td align="center">0.9081947</td>
|
||||
<td align="center">0.9821319</td>
|
||||
<td align="center">0.7274536</td>
|
||||
<td align="center">0.9177719</td>
|
||||
<td align="center">0.9781167</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7420746</td>
|
||||
<td align="center">0.9163074</td>
|
||||
<td align="center">0.9792037</td>
|
||||
<td align="center">0.7432570</td>
|
||||
<td align="center">0.9216285</td>
|
||||
<td align="center">0.9788804</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.7203947</td>
|
||||
<td align="center">0.7273819</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.7203947</td>
|
||||
<td align="center">0.7273819</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
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|
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|
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@ -192,7 +192,7 @@
|
||||
<h1>How to apply EUCAST rules</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>EUCAST.Rmd</code></div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to use the <em>G</em>-test</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>G_test.Rmd</code></div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to work with WHONET data</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>WHONET.Rmd</code></div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to get properties of an antibiotic</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>atc_property.Rmd</code></div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>Benchmarks</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>benchmarks.Rmd</code></div>
|
||||
@ -214,29 +214,18 @@
|
||||
<a class="sourceLine" id="cb2-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
|
||||
<a class="sourceLine" id="cb2-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a>
|
||||
<a class="sourceLine" id="cb2-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
|
||||
<a class="sourceLine" id="cb2-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
|
||||
<a class="sourceLine" id="cb2-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<a class="sourceLine" id="cb2-10" title="10"><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="cb2-11" title="11"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#> expr min lq mean median uq max</span></a>
|
||||
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#> as.mo("sau") 100.00 100.00 110.00 100.00 100.00 160.00</span></a>
|
||||
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#> as.mo("stau") 140.00 140.00 170.00 160.00 190.00 200.00</span></a>
|
||||
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#> as.mo("staaur") 99.00 100.00 100.00 100.00 100.00 110.00</span></a>
|
||||
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#> as.mo("S. aureus") 64.00 64.00 65.00 65.00 66.00 67.00</span></a>
|
||||
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#> as.mo("S. aureus") 65.00 65.00 70.00 66.00 66.00 110.00</span></a>
|
||||
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#> as.mo("STAAUR") 97.00 98.00 100.00 100.00 100.00 100.00</span></a>
|
||||
<a class="sourceLine" id="cb2-19" title="19"><span class="co">#> as.mo("Staphylococcus aureus") 35.00 35.00 36.00 36.00 37.00 38.00</span></a>
|
||||
<a class="sourceLine" id="cb2-20" title="20"><span class="co">#> as.mo("B_STPHY_AUR") 0.34 0.47 0.52 0.48 0.56 0.89</span></a>
|
||||
<a class="sourceLine" id="cb2-21" title="21"><span class="co">#> neval</span></a>
|
||||
<a class="sourceLine" id="cb2-22" title="22"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb2-23" title="23"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb2-24" title="24"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb2-25" title="25"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb2-26" title="26"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb2-27" title="27"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb2-28" title="28"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb2-29" title="29"><span class="co">#> 10</span></a></code></pre></div>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of <code><a href="../reference/as.mo.html">as.mo("B_STPHY_AUR")</a></code>, the input is already a valid MO code, so it only almost takes no time at all (476 millionths of a second).</p>
|
||||
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<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">3</span>)</a>
|
||||
<a class="sourceLine" id="cb2-10" title="10"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#> as.mo("sau") 42.9 43.2 43.9 44.0 44.2 45.1 10</span></a>
|
||||
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#> as.mo("stau") 86.8 87.0 88.9 87.3 88.2 101.0 10</span></a>
|
||||
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#> as.mo("staaur") 42.6 43.6 51.5 43.8 44.5 82.8 10</span></a>
|
||||
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#> as.mo("S. aureus") 23.2 23.3 31.0 23.5 23.6 61.8 10</span></a>
|
||||
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#> as.mo("S. aureus") 23.1 23.3 26.4 23.7 24.4 51.2 10</span></a>
|
||||
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#> as.mo("STAAUR") 42.8 43.4 44.5 44.3 44.5 47.8 10</span></a>
|
||||
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#> as.mo("Staphylococcus aureus") 14.3 14.5 20.4 14.8 16.0 64.6 10</span></a></code></pre></div>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found.</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>Mycoplasma leonicaptivi</em> (<code>B_MYCPL_LEO</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">M.leonicaptivi <-<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">"myle"</span>),</a>
|
||||
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"mycleo"</span>),</a>
|
||||
@ -244,134 +233,127 @@
|
||||
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. leonicaptivi"</span>),</a>
|
||||
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MYCLEO"</span>),</a>
|
||||
<a class="sourceLine" id="cb3-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Mycoplasma leonicaptivi"</span>),</a>
|
||||
<a class="sourceLine" id="cb3-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_MYCPL_LEO"</span>),</a>
|
||||
<a class="sourceLine" id="cb3-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(M.leonicaptivi, <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="cb3-10" title="10"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#> expr min lq mean median uq max</span></a>
|
||||
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#> as.mo("myle") 210.00 220.00 240.0 230.00 260.00 310</span></a>
|
||||
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#> as.mo("mycleo") 610.00 630.00 680.0 680.00 720.00 770</span></a>
|
||||
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#> as.mo("M. leonicaptivi") 370.00 370.00 390.0 390.00 410.00 410</span></a>
|
||||
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#> as.mo("M. leonicaptivi") 350.00 350.00 390.0 390.00 410.00 480</span></a>
|
||||
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#> as.mo("MYCLEO") 630.00 650.00 680.0 670.00 680.00 880</span></a>
|
||||
<a class="sourceLine" id="cb3-17" title="17"><span class="co">#> as.mo("Mycoplasma leonicaptivi") 250.00 250.00 260.0 250.00 260.00 290</span></a>
|
||||
<a class="sourceLine" id="cb3-18" title="18"><span class="co">#> as.mo("B_MYCPL_LEO") 0.35 0.43 5.6 0.69 0.75 50</span></a>
|
||||
<a class="sourceLine" id="cb3-19" title="19"><span class="co">#> neval</span></a>
|
||||
<a class="sourceLine" id="cb3-20" title="20"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb3-21" title="21"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb3-22" title="22"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb3-23" title="23"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb3-24" title="24"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb3-25" title="25"><span class="co">#> 10</span></a>
|
||||
<a class="sourceLine" id="cb3-26" title="26"><span class="co">#> 10</span></a></code></pre></div>
|
||||
<p>That takes 4.7 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:</p>
|
||||
<a class="sourceLine" id="cb3-7" title="7"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<a class="sourceLine" id="cb3-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(M.leonicaptivi, <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="cb3-9" title="9"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#> as.mo("myle") 141 142 162 142 142 299 10</span></a>
|
||||
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#> as.mo("mycleo") 479 481 520 525 530 634 10</span></a>
|
||||
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#> as.mo("M. leonicaptivi") 241 242 273 263 281 382 10</span></a>
|
||||
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#> as.mo("M. leonicaptivi") 239 241 268 282 283 299 10</span></a>
|
||||
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#> as.mo("MYCLEO") 487 520 525 524 528 601 10</span></a>
|
||||
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#> as.mo("Mycoplasma leonicaptivi") 152 156 183 174 200 261 10</span></a></code></pre></div>
|
||||
<p>That takes 7.3 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.</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>Mycoplasma leonicaptivi</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>
|
||||
<a class="sourceLine" id="cb4-3" title="3"><span class="co"># highest value on y axis</span></a>
|
||||
<a class="sourceLine" id="cb4-4" title="4">max_y_axis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Extremes">max</a></span>(S.aureus<span class="op">$</span>time, M.leonicaptivi<span class="op">$</span>time, <span class="dt">na.rm =</span> <span class="ot">TRUE</span>) <span class="op">/</span><span class="st"> </span><span class="fl">1e6</span></a>
|
||||
<a class="sourceLine" id="cb4-5" title="5"></a>
|
||||
<a class="sourceLine" id="cb4-6" title="6"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(S.aureus, <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>, <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylim =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, max_y_axis),</a>
|
||||
<a class="sourceLine" id="cb4-7" title="7"> <span class="dt">main =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/expression">expression</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Benchmark of "</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/plotmath">italic</a></span>(<span class="st">"Staphylococcus aureus"</span>))))</a></code></pre></div>
|
||||
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></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">"M. leonicaptivi"</span>),</a>
|
||||
<a class="sourceLine" id="cb4-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Mycoplasma leonicaptivi"</span>),</a>
|
||||
<a class="sourceLine" id="cb4-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
|
||||
<a class="sourceLine" id="cb4-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Prevotella brevis"</span>),</a>
|
||||
<a class="sourceLine" id="cb4-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
|
||||
<a class="sourceLine" id="cb4-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Escherichia coli"</span>),</a>
|
||||
<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">50</span>),</a>
|
||||
<a class="sourceLine" id="cb4-10" title="10"> <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"s"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>,</a>
|
||||
<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>,</a>
|
||||
<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>
|
||||
<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/graphics/topics/boxplot">boxplot</a></span>(M.leonicaptivi, <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>, <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylim =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, max_y_axis),</a>
|
||||
<a class="sourceLine" id="cb5-2" title="2"> <span class="dt">main =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/expression">expression</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Benchmark of "</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/plotmath">italic</a></span>(<span class="st">"Mycoplasma leonicaptivi"</span>))))</a></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
|
||||
<p>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>
|
||||
<p>Uncommon microorganisms take a lot more time than common microorganisms. 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 mean that unique values 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 500,000 random MO codes from the septic_patients data set</span></a>
|
||||
<a class="sourceLine" id="cb6-3" title="3">x =<span class="st"> </span>septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb6-4" title="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb6-5" title="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(mo)</a>
|
||||
<a class="sourceLine" id="cb6-6" title="6"> </a>
|
||||
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># got the right length?</span></a>
|
||||
<a class="sourceLine" id="cb6-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#> [1] 500000</span></a>
|
||||
<a class="sourceLine" id="cb6-10" title="10"></a>
|
||||
<a class="sourceLine" id="cb6-11" title="11"><span class="co"># and how many unique values do we have?</span></a>
|
||||
<a class="sourceLine" id="cb6-12" title="12"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb6-13" title="13"><span class="co">#> [1] 95</span></a>
|
||||
<a class="sourceLine" id="cb6-14" title="14"></a>
|
||||
<a class="sourceLine" id="cb6-15" title="15"><span class="co"># now let's see:</span></a>
|
||||
<a class="sourceLine" id="cb6-16" title="16">run_it <-<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="cb6-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<a class="sourceLine" id="cb6-18" 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">3</span>)</a>
|
||||
<a class="sourceLine" id="cb6-19" title="19"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb6-20" title="20"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb6-21" title="21"><span class="co">#> mo_fullname(x) 487 499 527 535 538 573 10</span></a></code></pre></div>
|
||||
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.54 seconds (535 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 500,000 random MO codes from the septic_patients data set</span></a>
|
||||
<a class="sourceLine" id="cb5-3" title="3">x =<span class="st"> </span>septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb5-4" title="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb5-5" title="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(mo)</a>
|
||||
<a class="sourceLine" id="cb5-6" title="6"> </a>
|
||||
<a class="sourceLine" id="cb5-7" title="7"><span class="co"># got the right length?</span></a>
|
||||
<a class="sourceLine" id="cb5-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb5-9" title="9"><span class="co">#> [1] 500000</span></a>
|
||||
<a class="sourceLine" id="cb5-10" title="10"></a>
|
||||
<a class="sourceLine" id="cb5-11" title="11"><span class="co"># and how many unique values do we have?</span></a>
|
||||
<a class="sourceLine" id="cb5-12" title="12"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb5-13" title="13"><span class="co">#> [1] 95</span></a>
|
||||
<a class="sourceLine" id="cb5-14" title="14"></a>
|
||||
<a class="sourceLine" id="cb5-15" title="15"><span class="co"># now let's see:</span></a>
|
||||
<a class="sourceLine" id="cb5-16" title="16">run_it <-<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="cb5-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<a class="sourceLine" id="cb5-18" 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">3</span>)</a>
|
||||
<a class="sourceLine" id="cb5-19" title="19"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb5-20" title="20"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb5-21" title="21"><span class="co">#> mo_fullname(x) 400 405 463 441 533 558 10</span></a></code></pre></div>
|
||||
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.44 seconds (441 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 <-<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>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">run_it <-<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">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#> A 39.000 39.80 40.000 40.100 40.300 41.100 10</span></a>
|
||||
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#> B 24.400 24.70 25.000 24.900 25.200 25.600 10</span></a>
|
||||
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#> C 0.294 0.39 0.422 0.401 0.505 0.535 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 0.0004 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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it <-<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">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">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb7-8" title="8"><span class="co">#> A 65.500 66.100 66.200 66.300 66.500 66.700 10</span></a>
|
||||
<a class="sourceLine" id="cb7-9" title="9"><span class="co">#> B 61.000 61.200 61.900 61.700 62.300 64.500 10</span></a>
|
||||
<a class="sourceLine" id="cb7-10" title="10"><span class="co">#> C 0.329 0.335 0.461 0.527 0.551 0.556 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 0.0005 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 <-<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">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb8-12" title="12"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb8-13" title="13"><span class="co">#> A 0.288 0.372 0.440 0.418 0.481 0.662 10</span></a>
|
||||
<a class="sourceLine" id="cb8-14" title="14"><span class="co">#> B 0.281 0.294 0.364 0.369 0.411 0.461 10</span></a>
|
||||
<a class="sourceLine" id="cb8-15" title="15"><span class="co">#> C 0.390 0.493 0.563 0.550 0.645 0.731 10</span></a>
|
||||
<a class="sourceLine" id="cb8-16" title="16"><span class="co">#> D 0.244 0.269 0.733 0.337 0.347 4.420 10</span></a>
|
||||
<a class="sourceLine" id="cb8-17" title="17"><span class="co">#> E 0.283 0.344 0.368 0.363 0.410 0.434 10</span></a>
|
||||
<a class="sourceLine" id="cb8-18" title="18"><span class="co">#> F 0.250 0.319 0.343 0.339 0.354 0.492 10</span></a>
|
||||
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#> G 0.286 0.329 0.363 0.340 0.392 0.496 10</span></a>
|
||||
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#> H 0.292 0.305 0.365 0.359 0.421 0.459 10</span></a></code></pre></div>
|
||||
<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">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb7-12" title="12"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#> A 0.298 0.327 0.398 0.400 0.452 0.535 10</span></a>
|
||||
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#> B 0.251 0.287 0.339 0.344 0.377 0.436 10</span></a>
|
||||
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#> C 0.293 0.403 0.451 0.487 0.500 0.537 10</span></a>
|
||||
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#> D 0.250 0.262 0.300 0.277 0.336 0.395 10</span></a>
|
||||
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#> E 0.249 0.261 0.306 0.313 0.344 0.384 10</span></a>
|
||||
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#> F 0.273 0.283 0.325 0.326 0.338 0.420 10</span></a>
|
||||
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#> G 0.238 0.293 0.312 0.325 0.342 0.356 10</span></a>
|
||||
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#> H 0.250 0.262 0.304 0.316 0.337 0.358 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">#> [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">#> [1] "Staphylococcus coagulasa negativo (CoNS)"</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">#> [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 <-<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">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb9-20" title="20"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb9-21" title="21"><span class="co">#> en 24.41 25.27 26.34 25.41 26.92 30.60 10</span></a>
|
||||
<a class="sourceLine" id="cb9-22" title="22"><span class="co">#> de 35.53 35.76 36.76 35.98 37.20 41.19 10</span></a>
|
||||
<a class="sourceLine" id="cb9-23" title="23"><span class="co">#> nl 34.51 35.55 39.93 35.60 40.15 69.76 10</span></a>
|
||||
<a class="sourceLine" id="cb9-24" title="24"><span class="co">#> es 34.36 35.98 44.29 37.46 39.98 73.16 10</span></a>
|
||||
<a class="sourceLine" id="cb9-25" title="25"><span class="co">#> it 35.78 36.22 37.44 36.75 38.70 40.78 10</span></a>
|
||||
<a class="sourceLine" id="cb9-26" title="26"><span class="co">#> fr 35.45 35.71 36.09 35.79 36.15 37.93 10</span></a>
|
||||
<a class="sourceLine" id="cb9-27" title="27"><span class="co">#> pt 35.10 35.44 44.61 35.76 39.68 77.27 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">#> [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">#> [1] "Staphylococcus coagulasa negativo (CoNS)"</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">#> [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 <-<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">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#> en 10.78 11.11 11.15 11.14 11.30 11.41 10</span></a>
|
||||
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#> de 19.60 19.65 23.24 19.76 20.61 52.47 10</span></a>
|
||||
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#> nl 19.14 19.71 19.75 19.72 19.87 20.22 10</span></a>
|
||||
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#> es 19.64 19.73 28.36 20.60 25.91 64.67 10</span></a>
|
||||
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#> it 19.33 19.49 23.13 19.68 19.97 52.72 10</span></a>
|
||||
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#> fr 19.43 19.54 20.08 19.72 20.60 21.46 10</span></a>
|
||||
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#> pt 19.34 19.66 23.15 19.80 20.48 52.40 10</span></a></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
Binary file not shown.
|
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@ -192,7 +192,7 @@
|
||||
<h1>How to create frequency tables</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>freq.Rmd</code></div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to get properties of a microorganism</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>mo_property.Rmd</code></div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to predict antimicrobial resistance</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 February 2019</h4>
|
||||
<h4 class="date">22 February 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
|
||||
|
||||
Reference in New Issue
Block a user