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2
DESCRIPTION

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
Package: AMR
Version: 0.7.1.9024
Version: 0.7.1.9026
Date: 2019-08-06
Title: Antimicrobial Resistance Analysis
Authors@R: c(

1
NAMESPACE

@ -272,3 +272,4 @@ importFrom(stats,pchisq) @@ -272,3 +272,4 @@ importFrom(stats,pchisq)
importFrom(stats,predict)
importFrom(utils,browseURL)
importFrom(utils,installed.packages)
importFrom(utils,menu)

2
NEWS.md

@ -1,4 +1,4 @@ @@ -1,4 +1,4 @@
# AMR 0.7.1.9024
# AMR 0.7.1.9026
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

434
docs/articles/AMR.html

@ -40,7 +40,7 @@ @@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
</span>
</div>
@ -185,7 +185,7 @@ @@ -185,7 +185,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 July 2019</h4>
<h4 class="date">06 August 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -194,7 +194,7 @@ @@ -194,7 +194,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 July 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 06 August 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -210,21 +210,21 @@ @@ -210,21 +210,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-07-29</td>
<td align="center">2019-08-06</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-07-29</td>
<td align="center">2019-08-06</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-07-29</td>
<td align="center">2019-08-06</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -320,10 +320,10 @@ @@ -320,10 +320,10 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-01-19</td>
<td align="center">U10</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">2017-03-10</td>
<td align="center">Q5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -331,57 +331,57 @@ @@ -331,57 +331,57 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-09-03</td>
<td align="center">T7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">2011-12-26</td>
<td align="center">G6</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-12-04</td>
<td align="center">U5</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2011-07-01</td>
<td align="center">L6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-06-26</td>
<td align="center">O1</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2015-08-22</td>
<td align="center">A9</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-08-04</td>
<td align="center">G2</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2017-03-16</td>
<td align="center">H1</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-05-10</td>
<td align="center">W8</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">2017-06-20</td>
<td align="center">V2</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@ -406,8 +406,8 @@ @@ -406,8 +406,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,424 52.1% 10,424 52.1%
# 2 F 9,576 47.9% 20,000 100.0%</code></pre>
# 1 M 10,366 51.8% 10,366 51.8%
# 2 F 9,634 48.2% 20,000 100.0%</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="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -437,14 +437,14 @@ @@ -437,14 +437,14 @@
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no new changes)</span></a>
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no new changes)</span></a>
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no new changes)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,485 new changes)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,439 new changes)</span></a>
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no new changes)</span></a>
<a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,312 new changes)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,329 new changes)</span></a>
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,746 new changes)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,679 new changes)</span></a>
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)</span></a>
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)</span></a>
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)</span></a>
@ -452,24 +452,24 @@ @@ -452,24 +452,24 @@
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no new changes)</span></a>
<a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,284 new changes)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (116 new changes)</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,347 new changes)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (114 new changes)</span></a>
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
<a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,581 out of 20,000 rows, making a total of 7,943 edits</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,589 out of 20,000 rows, making a total of 7,908 edits</span></a>
<a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,943 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 100 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,767 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,140 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 315 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,602 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 19 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,908 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 110 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,680 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,068 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 326 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,711 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 13 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-56" data-line-number="56"><span class="co"># Use 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 @@ @@ -497,8 +497,8 @@
<a class="sourceLine" id="cb17-3" 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="cb17-4" 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="cb17-5" 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="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,701 first isolates (28.5% of total)</span></a></code></pre></div>
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,681 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 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="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-2" 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 @@ @@ -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 S2, 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 C10, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -524,8 +524,8 @@ @@ -524,8 +524,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-05</td>
<td align="center">S2</td>
<td align="center">2010-07-24</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -535,10 +535,10 @@ @@ -535,10 +535,10 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-09</td>
<td align="center">S2</td>
<td align="center">2010-12-03</td>
<td align="center">C10</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>
@ -546,21 +546,21 @@ @@ -546,21 +546,21 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-08-25</td>
<td align="center">S2</td>
<td align="center">2010-12-19</td>
<td align="center">C10</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-20</td>
<td align="center">S2</td>
<td align="center">2011-02-18</td>
<td align="center">C10</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>
@ -568,19 +568,19 @@ @@ -568,19 +568,19 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-10-11</td>
<td align="center">S2</td>
<td align="center">2011-06-26</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-02-11</td>
<td align="center">S2</td>
<td align="center">2011-06-28</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -590,43 +590,43 @@ @@ -590,43 +590,43 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-02-24</td>
<td align="center">S2</td>
<td align="center">2011-06-30</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-12</td>
<td align="center">S2</td>
<td align="center">2011-08-29</td>
<td align="center">C10</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">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-04-21</td>
<td align="center">S2</td>
<td align="center">2011-10-03</td>
<td align="center">C10</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">2011-05-04</td>
<td align="center">S2</td>
<td align="center">2011-12-30</td>
<td align="center">C10</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>
@ -645,7 +645,7 @@ @@ -645,7 +645,7 @@
<a class="sourceLine" id="cb20-7" 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="cb20-8" 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="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,136 first weighted isolates (75.7% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,027 first weighted isolates (75.1% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -662,8 +662,8 @@ @@ -662,8 +662,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-05</td>
<td align="center">S2</td>
<td align="center">2010-07-24</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -674,34 +674,34 @@ @@ -674,34 +674,34 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-09</td>
<td align="center">S2</td>
<td align="center">2010-12-03</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-08-25</td>
<td align="center">S2</td>
<td align="center">2010-12-19</td>
<td align="center">C10</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-20</td>
<td align="center">S2</td>
<td align="center">2011-02-18</td>
<td align="center">C10</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>
@ -710,20 +710,20 @@ @@ -710,20 +710,20 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-10-11</td>
<td align="center">S2</td>
<td align="center">2011-06-26</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-02-11</td>
<td align="center">S2</td>
<td align="center">2011-06-28</td>
<td align="center">C10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -734,46 +734,46 @@ @@ -734,46 +734,46 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-02-24</td>
<td align="center">S2</td>
<td align="center">2011-06-30</td>
<td align="center">C10</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">8</td>
<td align="center">2011-03-12</td>
<td align="center">S2</td>
<td align="center">2011-08-29</td>
<td align="center">C10</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">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-04-21</td>
<td align="center">S2</td>
<td align="center">2011-10-03</td>
<td align="center">C10</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">2011-05-04</td>
<td align="center">S2</td>
<td align="center">2011-12-30</td>
<td align="center">C10</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>
@ -782,11 +782,11 @@ @@ -782,11 +782,11 @@
</tr>
</tbody>
</table>
<p>Instead of 2, now 7 isolates are flagged. In total, 75.7% of all isolates are marked ‘first weighted’ - 47.2% 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, of all isolates are marked ‘first weighted’ - 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="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</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="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,136 isolates for analysis.</p>
<p>So we end up with 15,027 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-2" 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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -811,15 +811,15 @@ @@ -811,15 +811,15 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>2</td>
<td align="center">2011-09-03</td>
<td align="center">T7</td>
<td align="center">Hospital B</td>
<td>1</td>
<td align="center">2017-03-10</td>
<td align="center">Q5</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</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">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -827,83 +827,83 @@ @@ -827,83 +827,83 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>3</td>
<td align="center">2011-12-04</td>
<td align="center">U5</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td>2</td>
<td align="center">2011-12-26</td>
<td align="center">G6</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>4</td>
<td align="center">2014-06-26</td>
<td align="center">O1</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td>
<td>3</td>
<td align="center">2011-07-01</td>
<td align="center">L6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2012-08-04</td>
<td align="center">G2</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>6</td>
<td align="center">2017-06-20</td>
<td align="center">V2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">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>7</td>
<td align="center">2012-11-12</td>
<td align="center">G6</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">2012-02-10</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</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 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">2017-07-19</td>
<td align="center">G4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">2010-05-01</td>
<td align="center">E1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -925,7 +925,7 @@ @@ -925,7 +925,7 @@
<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">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,136 (of which NA: 0 = 0.00%)<br>
Length: 15,027 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -942,33 +942,33 @@ 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">7,458</td>
<td align="right">49.3%</td>
<td align="right">7,458</td>
<td align="right">49.3%</td>
<td align="right">7,456</td>
<td align="right">49.6%</td>
<td align="right">7,456</td>
<td align="right">49.6%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,739</td>
<td align="right">3,709</td>
<td align="right">24.7%</td>
<td align="right">11,197</td>
<td align="right">74.0%</td>
<td align="right">11,165</td>
<td align="right">74.3%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,362</td>
<td align="right">15.6%</td>
<td align="right">13,559</td>
<td align="right">89.6%</td>
<td align="right">2,267</td>
<td align="right">15.1%</td>
<td align="right">13,432</td>
<td align="right">89.4%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,577</td>
<td align="right">10.4%</td>
<td align="right">15,136</td>
<td align="right">1,595</td>
<td align="right">10.6%</td>
<td align="right">15,027</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -979,7 +979,7 @@ Longest: 24</p> @@ -979,7 +979,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</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">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.462936</span></a></code></pre></div>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4685566</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="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb27-2" 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">%&gt;%</span><span class="st"> </span></a>
@ -992,19 +992,19 @@ Longest: 24</p> @@ -992,19 +992,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4701912</td>
<td align="center">0.4574111</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4536024</td>
<td align="center">0.4789054</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4589011</td>
<td align="center">0.4639895</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4714194</td>
<td align="center">0.4705098</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p> @@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4701912</td>
<td align="center">4445</td>
<td align="center">0.4574111</td>
<td align="center">4473</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4536024</td>
<td align="center">5302</td>
<td align="center">0.4789054</td>
<td align="center">5262</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4589011</td>
<td align="center">2275</td>
<td align="center">0.4639895</td>
<td align="center">2291</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4714194</td>
<td align="center">3114</td>
<td align="center">0.4705098</td>
<td align="center">3001</td>
</tr>
</tbody>
</table>
@ -1058,27 +1058,27 @@ Longest: 24</p> @@ -1058,27 +1058,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9249128</td>
<td align="center">0.8924645</td>
<td align="center">0.9945025</td>
<td align="center">0.9244903</td>
<td align="center">0.8964592</td>
<td align="center">0.9936964</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8338618</td>
<td align="center">0.8928345</td>
<td align="center">0.9822448</td>
<td align="center">0.8244514</td>
<td align="center">0.9059561</td>
<td align="center">0.9811912</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9152180</td>
<td align="center">0.9184274</td>
<td align="center">0.9946510</td>
<td align="center">0.9266649</td>
<td align="center">0.9201941</td>
<td align="center">0.9935293</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6147333</td>
<td align="center">0.6060873</td>
<td align="center">0.0000000</td>
<td align="center">0.6147333</td>
<td align="center">0.6060873</td>
</tr>
</tbody>
</table>

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docs/articles/MDR.html

@ -40,7 +40,7 @@ @@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
</span>
</div>
@ -185,7 +185,7 @@ @@ -185,7 +185,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">29 July 2019</h4>
<h4 class="date">06 August 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -228,16 +228,16 @@ @@ -228,16 +228,16 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 S S S R S S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R S R R I R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 S R R R I R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S R I I R</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R S R S S R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R S R R S R</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R R S R S S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R R S R S S</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R S R S S R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 R I S R R R</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 I S S R I S</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R R R S I S</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 I</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 I</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
@ -272,39 +272,39 @@ Unique: 5</p> @@ -272,39 +272,39 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3225</td>
<td align="right">64.5%</td>
<td align="right">3225</td>
<td align="right">64.5%</td>
<td align="right">3264</td>
<td align="right">65.3%</td>
<td align="right">3264</td>
<td align="right">65.3%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">644</td>
<td align="right">12.9%</td>
<td align="right">3869</td>
<td align="right">77.4%</td>
<td align="right">627</td>
<td align="right">12.5%</td>
<td align="right">3891</td>
<td align="right">77.8%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">626</td>
<td align="right">12.5%</td>
<td align="right">4495</td>
<td align="right">89.9%</td>
<td align="right">607</td>
<td align="right">12.1%</td>
<td align="right">4498</td>
<td align="right">90.0%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">288</td>
<td align="right">5.8%</td>
<td align="right">4783</td>
<td align="right">4786</td>
<td align="right">95.7%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">217</td>
<td align="right">214</td>
<td align="right">4.3%</td>
<td align="right">5000</td>
<td align="right">100.0%</td>

6
docs/articles/WHONET.html

@ -40,7 +40,7 @@ @@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
</span>
</div>
@ -185,7 +185,7 @@ @@ -185,7 +185,7 @@