(v0.8.0.9029) cleanup
@ -41,7 +41,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -321,71 +321,71 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-01-11</td>
|
||||
<td align="center">N1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">2015-05-08</td>
|
||||
<td align="center">P3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-11-03</td>
|
||||
<td align="center">Y8</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">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-12-17</td>
|
||||
<td align="center">D2</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">M</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-07-05</td>
|
||||
<td align="center">L5</td>
|
||||
<td align="center">2013-09-06</td>
|
||||
<td align="center">U9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2015-11-16</td>
|
||||
<td align="center">E7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-04-18</td>
|
||||
<td align="center">F4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-12-23</td>
|
||||
<td align="center">C5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">2010-04-22</td>
|
||||
<td align="center">L4</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-06-29</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-07-01</td>
|
||||
<td align="center">N10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Now, let’s start the cleaning and the analysis!</p>
|
||||
@ -406,8 +406,8 @@
|
||||
#
|
||||
# Item Count Percent Cum. Count Cum. Percent
|
||||
# --- ----- ------- -------- ----------- -------------
|
||||
# 1 M 10,264 51.32% 10,264 51.32%
|
||||
# 2 F 9,736 48.68% 20,000 100.00%</code></pre>
|
||||
# 1 M 10,417 52.09% 10,417 52.09%
|
||||
# 2 F 9,583 47.92% 20,000 100.00%</code></pre>
|
||||
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers 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" data-line-number="1">data <-<span class="st"> </span>data <span class="op">%>%</span></a>
|
||||
@ -437,14 +437,14 @@
|
||||
<a class="sourceLine" id="cb14-18" data-line-number="18"><span class="co"># Pasteurella multocida (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-19" data-line-number="19"><span class="co"># Staphylococcus (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,477 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,545 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-22" data-line-number="22"><span class="co"># Viridans group streptococci (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-23" data-line-number="23"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb14-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
|
||||
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,306 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,309 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,791 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,733 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
|
||||
@ -452,24 +452,24 @@
|
||||
<a class="sourceLine" id="cb14-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-34" data-line-number="34"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb14-35" data-line-number="35"><span class="co"># Other rules</span></a>
|
||||
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,203 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (104 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,194 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (121 values changed)</span></a>
|
||||
<a class="sourceLine" id="cb14-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-42" data-line-number="42"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb14-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
|
||||
<a class="sourceLine" id="cb14-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,529 out of 20,000 rows, making a total of 7,881 edits</span></a>
|
||||
<a class="sourceLine" id="cb14-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,489 out of 20,000 rows, making a total of 7,902 edits</span></a>
|
||||
<a class="sourceLine" id="cb14-45" data-line-number="45"><span class="co"># => added 0 test results</span></a>
|
||||
<a class="sourceLine" id="cb14-46" data-line-number="46"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># => changed 7,881 test results</span></a>
|
||||
<a class="sourceLine" id="cb14-48" data-line-number="48"><span class="co"># - 102 test results changed from S to I</span></a>
|
||||
<a class="sourceLine" id="cb14-49" data-line-number="49"><span class="co"># - 4,800 test results changed from S to R</span></a>
|
||||
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># - 1,035 test results changed from I to S</span></a>
|
||||
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 291 test results changed from I to R</span></a>
|
||||
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 1,625 test results changed from R to S</span></a>
|
||||
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 28 test results changed from R to I</span></a>
|
||||
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># => changed 7,902 test results</span></a>
|
||||
<a class="sourceLine" id="cb14-48" data-line-number="48"><span class="co"># - 118 test results changed from S to I</span></a>
|
||||
<a class="sourceLine" id="cb14-49" data-line-number="49"><span class="co"># - 4,776 test results changed from S to R</span></a>
|
||||
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># - 1,063 test results changed from I to S</span></a>
|
||||
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 318 test results changed from I to R</span></a>
|
||||
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 1,603 test results changed from R to S</span></a>
|
||||
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 24 test results changed from R to I</span></a>
|
||||
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
|
||||
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb14-56" data-line-number="56"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
|
||||
@ -497,8 +497,8 @@
|
||||
<a class="sourceLine" id="cb16-3" data-line-number="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" data-line-number="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" data-line-number="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" data-line-number="6"><span class="co"># => Found 5,674 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>
|
||||
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># => Found 5,696 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>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb17-2" data-line-number="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>
|
||||
@ -508,7 +508,7 @@
|
||||
<div id="first-weighted-isolates" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
|
||||
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient S8, sorted on date:</p>
|
||||
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient P1, sorted on date:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">isolate</th>
|
||||
@ -524,19 +524,19 @@
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-27</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-01-26</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-06-01</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-04-19</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -546,30 +546,30 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-09-13</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-04-24</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-09-27</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-06-11</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-10-15</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-11-24</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -579,8 +579,8 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-12-25</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-12-11</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -590,19 +590,19 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-02-06</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-12-23</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-03-27</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2011-01-14</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -612,25 +612,25 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-05-14</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2011-01-19</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-09-12</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2011-01-26</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -645,7 +645,7 @@
|
||||
<a class="sourceLine" id="cb19-7" data-line-number="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" data-line-number="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" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></a>
|
||||
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># => Found 15,253 first weighted isolates (76.3% of total)</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># => Found 15,241 first weighted isolates (76.2% of total)</span></a></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">isolate</th>
|
||||
@ -662,56 +662,56 @@
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-27</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-01-26</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-06-01</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-04-19</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-09-13</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">B_ESCHR_COLI</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">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-09-27</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-04-24</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-06-11</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-10-15</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-11-24</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -722,8 +722,8 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-12-25</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-12-11</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -734,35 +734,35 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-02-06</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2010-12-23</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-03-27</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2011-01-14</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-05-14</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2011-01-19</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
@ -770,23 +770,23 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-09-12</td>
|
||||
<td align="center">S8</td>
|
||||
<td align="center">2011-01-26</td>
|
||||
<td align="center">P1</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Instead of 2, now 6 isolates are flagged. In total, 76.3% of all isolates are marked ‘first weighted’ - 47.9% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
|
||||
<p>Instead of 2, now 10 isolates are flagged. In total, 76.2% of all isolates are marked ‘first weighted’ - 47.7% 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" data-line-number="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb20-2" data-line-number="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 15,253 isolates for analysis.</p>
|
||||
<p>So we end up with 15,241 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" data-line-number="1">data_1st <-<span class="st"> </span>data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb21-2" data-line-number="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://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</a></code></pre></div>
|
||||
@ -811,16 +811,16 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>2</td>
|
||||
<td align="center">2010-12-17</td>
|
||||
<td align="center">D2</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td>1</td>
|
||||
<td align="center">2015-05-08</td>
|
||||
<td align="center">P3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
@ -828,82 +828,82 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>3</td>
|
||||
<td align="center">2016-07-05</td>
|
||||
<td align="center">L5</td>
|
||||
<td align="center">2013-09-06</td>
|
||||
<td align="center">U9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</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>4</td>
|
||||
<td align="center">2016-12-23</td>
|
||||
<td align="center">C5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td>5</td>
|
||||
<td align="center">2011-04-18</td>
|
||||
<td align="center">F4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</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>5</td>
|
||||
<td align="center">2011-06-29</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td>7</td>
|
||||
<td align="center">2016-10-10</td>
|
||||
<td align="center">S10</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">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>
|
||||
<tr class="odd">
|
||||
<td>6</td>
|
||||
<td align="center">2011-07-01</td>
|
||||
<td align="center">N10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td>8</td>
|
||||
<td align="center">2010-01-21</td>
|
||||
<td align="center">R3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</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">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>8</td>
|
||||
<td align="center">2010-01-02</td>
|
||||
<td align="center">X9</td>
|
||||
<td>9</td>
|
||||
<td align="center">2011-11-23</td>
|
||||
<td align="center">B7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">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">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -925,7 +925,7 @@
|
||||
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 15,253 (of which NA: 0 = 0%)<br>
|
||||
Length: 15,241 (of which NA: 0 = 0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -942,33 +942,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">7,529</td>
|
||||
<td align="right">49.36%</td>
|
||||
<td align="right">7,529</td>
|
||||
<td align="right">49.36%</td>
|
||||
<td align="right">7,593</td>
|
||||
<td align="right">49.82%</td>
|
||||
<td align="right">7,593</td>
|
||||
<td align="right">49.82%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">3,765</td>
|
||||
<td align="right">24.68%</td>
|
||||
<td align="right">11,294</td>
|
||||
<td align="right">74.04%</td>
|
||||
<td align="right">3,734</td>
|
||||
<td align="right">24.50%</td>
|
||||
<td align="right">11,327</td>
|
||||
<td align="right">74.32%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,350</td>
|
||||
<td align="right">15.41%</td>
|
||||
<td align="right">13,644</td>
|
||||
<td align="right">89.45%</td>
|
||||
<td align="right">2,327</td>
|
||||
<td align="right">15.27%</td>
|
||||
<td align="right">13,654</td>
|
||||
<td align="right">89.59%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,609</td>
|
||||
<td align="right">10.55%</td>
|
||||
<td align="right">15,253</td>
|
||||
<td align="right">1,587</td>
|
||||
<td align="right">10.41%</td>
|
||||
<td align="right">15,241</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -980,7 +980,7 @@ Longest: 24</p>
|
||||
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
|
||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX)</a>
|
||||
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4715794</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4724099</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" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb26-2" data-line-number="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>
|
||||
@ -993,19 +993,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4697103</td>
|
||||
<td align="center">0.4637681</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4727821</td>
|
||||
<td align="center">0.4776811</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4739112</td>
|
||||
<td align="center">0.4811697</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4705116</td>
|
||||
<td align="center">0.4694820</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1023,23 +1023,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4697103</td>
|
||||
<td align="center">4556</td>
|
||||
<td align="center">0.4637681</td>
|
||||
<td align="center">4554</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4727821</td>
|
||||
<td align="center">5309</td>
|
||||
<td align="center">0.4776811</td>
|
||||
<td align="center">5399</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4739112</td>
|
||||
<td align="center">2319</td>
|
||||
<td align="center">0.4811697</td>
|
||||
<td align="center">2257</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4705116</td>
|
||||
<td align="center">3069</td>
|
||||
<td align="center">0.4694820</td>
|
||||
<td align="center">3031</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1059,27 +1059,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.9246912</td>
|
||||
<td align="center">0.8918847</td>
|
||||
<td align="center">0.9929606</td>
|
||||
<td align="center">0.9212433</td>
|
||||
<td align="center">0.8984591</td>
|
||||
<td align="center">0.9927565</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8309509</td>
|
||||
<td align="center">0.9030454</td>
|
||||
<td align="center">0.9869484</td>
|
||||
<td align="center">0.8298677</td>
|
||||
<td align="center">0.8897290</td>
|
||||
<td align="center">0.9836169</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.9301461</td>
|
||||
<td align="center">0.9189907</td>
|
||||
<td align="center">0.9933599</td>
|
||||
<td align="center">0.9290305</td>
|
||||
<td align="center">0.9258168</td>
|
||||
<td align="center">0.9946438</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.6251064</td>
|
||||
<td align="center">0.6067899</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.6251064</td>
|
||||
<td align="center">0.6067899</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
Before Width: | Height: | Size: 63 KiB After Width: | Height: | Size: 64 KiB |
Before Width: | Height: | Size: 51 KiB After Width: | Height: | Size: 51 KiB |
Before Width: | Height: | Size: 102 KiB After Width: | Height: | Size: 102 KiB |
Before Width: | Height: | Size: 83 KiB After Width: | Height: | Size: 83 KiB |
@ -41,7 +41,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -187,7 +187,7 @@
|
||||
<h1>How to apply EUCAST rules</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">09 November 2019</h4>
|
||||
<h4 class="date">10 November 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>EUCAST.Rmd</code></div>
|
||||
|
@ -41,7 +41,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -187,7 +187,7 @@
|
||||
<h1>How to determine multi-drug resistance (MDR)</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">09 November 2019</h4>
|
||||
<h4 class="date">10 November 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>MDR.Rmd</code></div>
|
||||
@ -237,7 +237,7 @@ The German national guideline - Mueller et al. (2015) Antimicrobial Resistance a
|
||||
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...OK.</span></a>
|
||||
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability will be improved if these antimicrobial results would be available too: SAM (ampicillin/sulbactam), ATM (aztreonam), CTT (cefotetan), CPT (ceftaroline), DAP (daptomycin), DOR (doripenem), ETP (ertapenem), FUS (fusidic acid), GEH (gentamicin-high), LVX (levofloxacin), MNO (minocycline), NET (netilmicin), PLB (polymyxin B), QDA (quinupristin/dalfopristin), STH (streptomycin-high), TLV (telavancin), TCC (ticarcillin/clavulanic acid)</span></a>
|
||||
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># Table 1 - S. aureus ... OK</span></a>
|
||||
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># Table 1 - Staphylococcus aureus ... OK</span></a>
|
||||
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># Table 2 - Enterococcus spp. ... OK</span></a>
|
||||
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># Table 3 - Enterobacteriaceae ... OK</span></a>
|
||||
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Table 4 - Pseudomonas aeruginosa ... OK</span></a>
|
||||
@ -306,19 +306,19 @@ Unique: 2</p>
|
||||
<p>The data set now looks like this:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</a>
|
||||
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
|
||||
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1 S S R R S R</span></a>
|
||||
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2 S R S S R S</span></a>
|
||||
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3 R S R S R R</span></a>
|
||||
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4 S S R S S I</span></a>
|
||||
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5 R R S R S S</span></a>
|
||||
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6 S S R R R S</span></a>
|
||||
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1 S R S R I R</span></a>
|
||||
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2 I S R I R R</span></a>
|
||||
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3 S R S S S R</span></a>
|
||||
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4 R S S S R S</span></a>
|
||||
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5 S S S S I R</span></a>
|
||||
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6 I S R I S S</span></a>
|
||||
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># kanamycin</span></a>
|
||||
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># 1 S</span></a>
|
||||
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2 S</span></a>
|
||||
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2 R</span></a>
|
||||
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># 3 R</span></a>
|
||||
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4 R</span></a>
|
||||
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4 S</span></a>
|
||||
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># 5 S</span></a>
|
||||
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6 R</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</a></code></pre></div>
|
||||
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
|
||||
@ -335,7 +335,7 @@ Unique: 2</p>
|
||||
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Author: WHO (World Health Organization)</span></a>
|
||||
<a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
|
||||
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># => Found 4371 MDROs out of 5000 tested isolates (87.4%)</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># => Found 4320 MDROs out of 5000 tested isolates (86.4%)</span></a></code></pre></div>
|
||||
<p>Create a frequency table of the results:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
@ -356,40 +356,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3301</td>
|
||||
<td align="right">66.02%</td>
|
||||
<td align="right">3301</td>
|
||||
<td align="right">66.02%</td>
|
||||
<td align="right">3243</td>
|
||||
<td align="right">64.86%</td>
|
||||
<td align="right">3243</td>
|
||||
<td align="right">64.86%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">629</td>
|
||||
<td align="right">12.58%</td>
|
||||
<td align="right">3930</td>
|
||||
<td align="right">78.60%</td>
|
||||
<td align="right">680</td>
|
||||
<td align="right">13.60%</td>
|
||||
<td align="right">3923</td>
|
||||
<td align="right">78.46%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">596</td>
|
||||
<td align="right">11.92%</td>
|
||||
<td align="right">4526</td>
|
||||
<td align="right">90.52%</td>
|
||||
<td align="right">587</td>
|
||||
<td align="right">11.74%</td>
|
||||
<td align="right">4510</td>
|
||||
<td align="right">90.20%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">282</td>
|
||||
<td align="right">5.64%</td>
|
||||
<td align="right">4808</td>
|
||||
<td align="right">96.16%</td>
|
||||
<td align="right">302</td>
|
||||
<td align="right">6.04%</td>
|
||||
<td align="right">4812</td>
|
||||
<td align="right">96.24%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">192</td>
|
||||
<td align="right">3.84%</td>
|
||||
<td align="right">188</td>
|
||||
<td align="right">3.76%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
@ -41,7 +41,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -187,7 +187,7 @@
|
||||
<h1>How to work with WHONET data</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">09 November 2019</h4>
|
||||
<h4 class="date">10 November 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>WHONET.Rmd</code></div>
|
||||
|
@ -84,7 +84,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|