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as.mo improvements

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dr. M.S. (Matthijs) Berends 2019-02-25 16:07:21 +01:00
parent c506d2893b
commit f25a4b3679
8 changed files with 294 additions and 272 deletions
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15
R/mo.R
View File

@ -166,6 +166,21 @@
#' mutate(mo = as.mo(paste(genus, species)))
#' }
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source()) {
if (all(x %in% AMR::microorganisms$fullname)
& isFALSE(Becker)
& isFALSE(Lancefield)
& is.null(reference_df)) {
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
y <- microorganismsDT[prevalence == 1][data.table(fullname = x), on = "fullname", "mo"][[1]]
if (any(is.na(y))) {
y[is.na(y)] <- microorganismsDT[prevalence == 2][data.table(fullname = x[is.na(y)]), on = "fullname", "mo"][[1]]
}
if (any(is.na(y))) {
y[is.na(y)] <- microorganismsDT[prevalence == 3][data.table(fullname = x[is.na(y)]), on = "fullname", "mo"][[1]]
}
return(y)
}
# will be checked for mo class in validation
mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,

477
docs/articles/AMR.html
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@ -327,10 +327,32 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-07-18</td>
<td align="center">Z5</td>
<td align="center">2011-05-27</td>
<td align="center">C5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-08-22</td>
<td align="center">Q6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-03-11</td>
<td align="center">V9</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -338,19 +360,8 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-01-13</td>
<td align="center">P8</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-07-31</td>
<td align="center">K5</td>
<td align="center">2012-12-25</td>
<td align="center">A1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -359,31 +370,20 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-07-12</td>
<td align="center">U8</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-09-10</td>
<td align="center">Y1</td>
<td align="center">2011-09-17</td>
<td align="center">I5</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</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">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-07-30</td>
<td align="center">X10</td>
<td align="center">2017-05-19</td>
<td align="center">O7</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
@ -411,8 +411,8 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,383 51.9% 10,383 51.9%
#&gt; 2 F 9,617 48.1% 20,000 100.0%</code></pre>
#&gt; 1 M 10,437 52.2% 10,437 52.2%
#&gt; 2 F 9,563 47.8% 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>
@ -443,10 +443,10 @@
<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 (1340 changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1294 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 (2699 changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2675 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>
@ -462,9 +462,9 @@
<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 7,406 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,390 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 4,039 test results (0 to S; 0 to I; 4,039 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 3,969 test results (0 to S; 0 to I; 3,969 to R)</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -489,7 +489,7 @@
<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 5,676 first isolates (28.4% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,670 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>
@ -516,41 +516,41 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-12</td>
<td align="center">I7</td>
<td align="center">2010-03-10</td>
<td align="center">F7</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-30</td>
<td align="center">I7</td>
<td align="center">2010-03-12</td>
<td align="center">F7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</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>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-28</td>
<td align="center">I7</td>
<td align="center">2010-06-18</td>
<td align="center">F7</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="even">
<td align="center">4</td>
<td align="center">2010-07-08</td>
<td align="center">I7</td>
<td align="center">2010-10-16</td>
<td align="center">F7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -560,21 +560,21 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-22</td>
<td align="center">I7</td>
<td align="center">2010-11-12</td>
<td align="center">F7</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-04</td>
<td align="center">I7</td>
<td align="center">2010-11-24</td>
<td align="center">F7</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>
@ -582,10 +582,10 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-16</td>
<td align="center">I7</td>
<td align="center">2011-02-24</td>
<td align="center">F7</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>
@ -593,34 +593,34 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-31</td>
<td align="center">I7</td>
<td align="center">2011-03-30</td>
<td align="center">F7</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">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-05-25</td>
<td align="center">I7</td>
<td align="center">2011-08-09</td>
<td align="center">F7</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>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-08-25</td>
<td align="center">I7</td>
<td align="center">2011-08-14</td>
<td align="center">F7</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">S</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">#&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 15,935 first weighted isolates (79.7% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,887 first weighted isolates (79.4% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,70 +654,70 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-12</td>
<td align="center">I7</td>
<td align="center">2010-03-10</td>
<td align="center">F7</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-04-30</td>
<td align="center">I7</td>
<td align="center">2010-03-12</td>
<td align="center">F7</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>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-28</td>
<td align="center">I7</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">4</td>
<td align="center">2010-07-08</td>
<td align="center">I7</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>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-22</td>
<td align="center">I7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">I</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>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-06-18</td>
<td align="center">F7</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">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-10-16</td>
<td align="center">F7</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">5</td>
<td align="center">2010-11-12</td>
<td align="center">F7</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">2010-09-04</td>
<td align="center">I7</td>
<td align="center">2010-11-24</td>
<td align="center">F7</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>
@ -726,10 +726,10 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-16</td>
<td align="center">I7</td>
<td align="center">2011-02-24</td>
<td align="center">F7</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>
@ -738,47 +738,47 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-31</td>
<td align="center">I7</td>
<td align="center">2011-03-30</td>
<td align="center">F7</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">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-05-25</td>
<td align="center">I7</td>
<td align="center">2011-08-09</td>
<td align="center">F7</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-08-25</td>
<td align="center">I7</td>
<td align="center">2011-08-14</td>
<td align="center">F7</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 7 isolates are flagged. In total, 79.7% of all isolates are marked ‘first weighted’ - 51.3% 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, 79.4% of all isolates are marked ‘first weighted’ - 51.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="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 15,935 isolates for analysis.</p>
<p>So we end up with 15,887 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>
@ -786,6 +786,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -802,41 +803,12 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-07-18</td>
<td align="center">Z5</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">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-01-13</td>
<td align="center">P8</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">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="odd">
<td align="center">2014-07-31</td>
<td align="center">K5</td>
<td>1</td>
<td align="center">2011-05-27</td>
<td align="center">C5</td>
<td align="center">Hospital B</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>
@ -847,38 +819,25 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-07-12</td>
<td align="center">U8</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td>2</td>
<td align="center">2010-08-22</td>
<td align="center">Q6</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-09-10</td>
<td align="center">Y1</td>
<td align="center">Hospital B</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">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">2017-07-30</td>
<td align="center">X10</td>
<td>6</td>
<td align="center">2017-05-19</td>
<td align="center">O7</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
@ -891,6 +850,54 @@
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>8</td>
<td align="center">2011-01-19</td>
<td align="center">Q7</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="odd">
<td>9</td>
<td align="center">2014-06-24</td>
<td align="center">S9</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>10</td>
<td align="center">2011-10-01</td>
<td align="center">O10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</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 positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -908,9 +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">%&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> (15,935 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,887 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,935 (of which NA: 0 = 0.00%)<br>
Length: 15,887 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -927,33 +934,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,898</td>
<td align="right">49.6%</td>
<td align="right">7,898</td>
<td align="right">49.6%</td>
<td align="right">7,900</td>
<td align="right">49.7%</td>
<td align="right">7,900</td>
<td align="right">49.7%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">4,017</td>
<td align="right">25.2%</td>
<td align="right">11,915</td>
<td align="right">74.8%</td>
<td align="right">3,951</td>
<td align="right">24.9%</td>
<td align="right">11,851</td>
<td align="right">74.6%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,449</td>
<td align="right">15.4%</td>
<td align="right">14,364</td>
<td align="right">90.1%</td>
<td align="right">2,413</td>
<td align="right">15.2%</td>
<td align="right">14,264</td>
<td align="right">89.8%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,571</td>
<td align="right">9.9%</td>
<td align="right">15,935</td>
<td align="right">1,623</td>
<td align="right">10.2%</td>
<td align="right">15,887</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -964,7 +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">%&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] 0.4776279</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4763014</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 +984,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4740616</td>
<td align="center">0.4774125</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4748265</td>
<td align="center">0.4762754</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4910305</td>
<td align="center">0.4630957</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4777953</td>
<td align="center">0.4845070</td>
</tr>
</tbody>
</table>
@ -1007,23 +1014,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4740616</td>
<td align="center">4742</td>
<td align="center">0.4774125</td>
<td align="center">4715</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4748265</td>
<td align="center">5621</td>
<td align="center">0.4762754</td>
<td align="center">5606</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4910305</td>
<td align="center">2397</td>
<td align="center">0.4630957</td>
<td align="center">2371</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4777953</td>
<td align="center">3175</td>
<td align="center">0.4845070</td>
<td align="center">3195</td>
</tr>
</tbody>
</table>
@ -1043,27 +1050,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7295518</td>
<td align="center">0.9013674</td>
<td align="center">0.9772094</td>
<td align="center">0.7267089</td>
<td align="center">0.9002532</td>
<td align="center">0.9720253</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7517505</td>
<td align="center">0.9000637</td>
<td align="center">0.9789943</td>
<td align="center">0.7233518</td>
<td align="center">0.8983364</td>
<td align="center">0.9741220</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7353747</td>
<td align="center">0.9168534</td>
<td align="center">0.9788399</td>
<td align="center">0.7296887</td>
<td align="center">0.9248292</td>
<td align="center">0.9787396</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7390772</td>
<td align="center">0.7318690</td>
<td align="center">0.0000000</td>
<td align="center">0.7390772</td>
<td align="center">0.7318690</td>
</tr>
</tbody>
</table>

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@ -217,14 +217,14 @@
<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">#&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") 12.1 12.2 12.3 12.2 12.3 12.6 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 81.3 81.9 97.3 82.7 120.0 155.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 12.2 12.3 12.7 12.6 13.2 13.5 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 12.2 12.3 16.5 12.6 13.4 50.7 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 20.1 20.1 25.2 20.1 20.2 69.9 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 20.1 20.2 20.7 20.3 21.6 22.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 11.2 11.3 11.5 11.3 11.5 12.4 10</span></a></code></pre></div>
<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") 13.40 13.60 17.8 13.60 13.80 51.6 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 83.00 83.30 96.5 85.30 88.40 163.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 13.50 13.50 19.1 13.70 14.90 51.5 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 13.50 13.50 14.1 13.60 13.70 18.2 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 21.40 21.40 22.1 21.50 21.70 25.4 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 21.40 21.40 25.7 21.60 23.30 60.1 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 5.63 5.87 15.2 5.94 8.32 57.8 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 second input is the only one that has to be looked up thoroughly. All the others are known codes (the first is a WHONET code) or common laboratory codes, or common full organism names like the last one.</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>
@ -235,13 +235,13 @@
<a class="sourceLine" id="cb3-6" title="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<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">3</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") 446.0 452.0 478.0 486.0 488.0 506 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 446.0 446.0 471.0 467.0 489.0 528 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 76.5 77.1 87.4 77.2 85.4 127 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 76.9 76.9 81.4 77.1 79.1 116 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 67.6 67.7 80.0 67.9 106.0 112 10</span></a></code></pre></div>
<p>That takes 8.5 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="cb3-9" 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") 448.0 486.0 483.0 489.0 490.0 510.0 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 447.0 489.0 487.0 491.0 493.0 499.0 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 78.0 78.2 78.9 78.7 78.9 82.3 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 78.1 78.3 84.4 78.8 81.3 129.0 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 61.8 62.1 75.4 62.8 104.0 109.0 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>
@ -287,8 +287,8 @@
<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) 679 731 768 762 779 886 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.76 seconds (762 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#&gt; mo_fullname(x) 741 746 806 778 827 968 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.78 seconds (778 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -300,11 +300,11 @@
<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 10.200 10.400 10.800 10.700 10.900 12.00 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 20.700 20.800 21.000 20.900 21.100 22.30 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.305 0.313 0.454 0.441 0.568 0.72 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>
<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 10.200 10.300 10.600 10.400 11.00 11.300 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 20.500 20.700 21.300 21.400 22.00 22.100 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.308 0.504 0.589 0.591 0.73 0.863 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 0.0006 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 &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>
@ -317,14 +317,14 @@
<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 0.366 0.446 0.563 0.523 0.681 0.785 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.365 0.453 0.598 0.661 0.682 0.859 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.369 0.477 0.633 0.646 0.674 1.150 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.283 0.337 0.455 0.464 0.609 0.611 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.309 0.333 0.422 0.393 0.527 0.606 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.280 0.316 0.457 0.466 0.557 0.676 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.283 0.328 0.422 0.359 0.535 0.638 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.295 0.339 0.402 0.368 0.460 0.562 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.318 0.340 0.388 0.382 0.434 0.474 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.339 0.362 0.424 0.428 0.449 0.555 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.331 0.369 0.522 0.526 0.637 0.673 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.269 0.278 0.313 0.300 0.353 0.384 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.252 0.266 0.322 0.302 0.349 0.448 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.241 0.264 0.310 0.313 0.347 0.379 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.241 0.258 0.310 0.317 0.355 0.386 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.278 0.289 0.316 0.313 0.334 0.375 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">
@ -351,13 +351,13 @@
<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 13.28 13.65 27.39 31.90 36.32 47.03 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 21.46 22.08 32.62 22.15 45.37 80.16 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 21.54 22.09 29.93 22.23 44.86 55.15 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 21.53 22.09 28.80 22.10 22.16 57.05 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 22.00 22.16 23.19 22.28 23.35 27.89 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 22.15 22.17 26.42 22.34 23.48 45.54 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 22.05 22.09 28.13 22.31 23.76 55.38 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 13.23 13.57 16.92 13.69 13.73 46.78 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 22.09 22.20 25.72 22.32 23.16 55.31 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 21.66 22.03 22.12 22.15 22.20 22.52 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 21.67 22.07 22.32 22.16 22.45 23.26 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 21.64 21.86 22.35 22.21 22.48 23.90 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 21.70 22.10 28.72 22.21 22.33 55.28 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 21.78 22.12 28.83 22.19 22.21 55.99 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
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