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DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.0.9010
Date: 2019-06-16
Version: 0.7.0.9012
Date: 2019-06-18
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

1
NAMESPACE
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@ -301,6 +301,7 @@ importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,text)

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NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.0.9010
# AMR 0.7.0.9012
#### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:

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docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>

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docs/articles/AMR.html
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">15 June 2019</h4>
<h4 class="date">18 June 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -201,7 +201,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 15 June 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 18 June 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -217,21 +217,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-06-15</td>
<td align="center">2019-06-18</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">2019-06-15</td>
<td align="center">2019-06-18</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">2019-06-15</td>
<td align="center">2019-06-18</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,71 +327,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-06-23</td>
<td align="center">R10</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2012-05-24</td>
<td align="center">H8</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">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-04-09</td>
<td align="center">R1</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">2013-01-14</td>
<td align="center">S5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-01-27</td>
<td align="center">U10</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">2011-04-02</td>
<td align="center">G2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-05-23</td>
<td align="center">C4</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">2011-09-22</td>
<td align="center">B3</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-03-27</td>
<td align="center">W3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-06-14</td>
<td align="center">L5</td>
<td align="center">2015-07-30</td>
<td align="center">G10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-10-07</td>
<td align="center">X3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</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>
@ -411,8 +411,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,341 51.7% 10,341 51.7%
# 2 F 9,659 48.3% 20,000 100.0%</code></pre>
# 1 M 10,332 51.7% 10,332 51.7%
# 2 F 9,668 48.3% 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="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -442,14 +442,14 @@
<a class="sourceLine" id="cb14-18" title="18"><span class="co"># Pasteurella multocida (no new changes)</span></a>
<a class="sourceLine" id="cb14-19" title="19"><span class="co"># Staphylococcus (no new changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co"># Streptococcus groups A, B, C, G (no new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1,478 new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1,428 new changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co"># Viridans group streptococci (no new changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,340 new changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,339 new changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,785 new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,671 new changes)</span></a>
<a class="sourceLine" id="cb14-29" title="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="cb14-30" title="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="cb14-31" title="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)</span></a>
@ -457,24 +457,24 @@
<a class="sourceLine" id="cb14-33" title="33"><span class="co"># Table 13: Interpretive rules for quinolones (no new changes)</span></a>
<a class="sourceLine" id="cb14-34" title="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-35" title="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,164 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (105 new changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,233 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (92 new changes)</span></a>
<a class="sourceLine" id="cb14-38" title="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,519 out of 20,000 rows, making a total of 7,872 edits</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,456 out of 20,000 rows, making a total of 7,763 edits</span></a>
<a class="sourceLine" id="cb14-45" title="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-46" title="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,872 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 122 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,775 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,060 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 316 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,581 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 18 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,763 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 95 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,674 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,070 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 305 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,596 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 23 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-54" title="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-55" title="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-56" title="56"><span class="co"># Use verbose = TRUE to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -502,8 +502,8 @@
<a class="sourceLine" id="cb16-3" title="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" title="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,652 first isolates (28.3% of total)</span></a></code></pre></div>
<p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,673 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -513,7 +513,7 @@
<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 V3, 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 W10, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -529,21 +529,21 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-06</td>
<td align="center">V3</td>
<td align="center">2010-01-10</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-07-24</td>
<td align="center">V3</td>
<td align="center">2010-04-21</td>
<td align="center">W10</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>
@ -551,32 +551,32 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-26</td>
<td align="center">V3</td>
<td align="center">2010-05-14</td>
<td align="center">W10</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-21</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2011-05-06</td>
<td align="center">V3</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">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-06-04</td>
<td align="center">V3</td>
<td align="center">2010-06-09</td>
<td align="center">W10</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>
@ -584,41 +584,41 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-07-22</td>
<td align="center">V3</td>
<td align="center">2010-06-19</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-08-15</td>
<td align="center">V3</td>
<td align="center">2010-07-07</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-09-20</td>
<td align="center">V3</td>
<td align="center">2010-07-10</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-03-26</td>
<td align="center">V3</td>
<td align="center">2010-08-12</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -628,18 +628,18 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2012-06-01</td>
<td align="center">V3</td>
<td align="center">2010-10-15</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 3 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -650,7 +650,7 @@
<a class="sourceLine" id="cb19-7" title="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" title="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb19-9" title="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,202 first weighted isolates (76.0% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,099 first weighted isolates (75.5% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -667,58 +667,58 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-06</td>
<td align="center">V3</td>
<td align="center">2010-01-10</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-07-24</td>
<td align="center">V3</td>
<td align="center">2010-04-21</td>
<td align="center">W10</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">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-26</td>
<td align="center">V3</td>
<td align="center">2010-05-14</td>
<td align="center">W10</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">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">4</td>
<td align="center">2011-05-06</td>
<td align="center">V3</td>
<td align="center">2010-05-21</td>
<td align="center">W10</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">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-06-04</td>
<td align="center">V3</td>
<td align="center">2010-06-09</td>
<td align="center">W10</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>
@ -727,44 +727,44 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-07-22</td>
<td align="center">V3</td>
<td align="center">2010-06-19</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-08-15</td>
<td align="center">V3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-07-07</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-09-20</td>
<td align="center">V3</td>
<td align="center">2010-07-10</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-03-26</td>
<td align="center">V3</td>
<td align="center">2010-08-12</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -775,23 +775,23 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2012-06-01</td>
<td align="center">V3</td>
<td align="center">2010-10-15</td>
<td align="center">W10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 3, now 8 isolates are flagged. In total, 76% 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>Instead of 1, now 7 isolates are flagged. In total, 75.5% of all isolates are marked ‘first weighted’ - 47.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,202 isolates for analysis.</p>
<p>So we end up with 15,099 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -799,6 +799,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -815,68 +816,9 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-06-23</td>
<td align="center">R10</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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-04-09</td>
<td align="center">R1</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-01-27</td>
<td align="center">U10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-05-23</td>
<td align="center">C4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2015-03-27</td>
<td align="center">W3</td>
<td>2</td>
<td align="center">2013-01-14</td>
<td align="center">S5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
@ -890,12 +832,29 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-06-14</td>
<td align="center">L5</td>
<td align="center">Hospital A</td>
<td>3</td>
<td align="center">2011-04-02</td>
<td align="center">G2</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>4</td>
<td align="center">2011-09-22</td>
<td align="center">B3</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -904,6 +863,54 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2015-07-30</td>
<td align="center">G10</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2017-10-07</td>
<td align="center">X3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2015-11-01</td>
<td align="center">O1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -921,9 +928,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from <code>data_1st</code> (15,202 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from <code>data_1st</code> (15,099 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,202 (of which NA: 0 = 0.00%)<br>
Length: 15,099 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -940,33 +947,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,485</td>
<td align="right">49.2%</td>
<td align="right">7,485</td>
<td align="right">49.2%</td>
<td align="right">7,513</td>
<td align="right">49.8%</td>
<td align="right">7,513</td>
<td align="right">49.8%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,758</td>
<td align="right">24.7%</td>
<td align="right">11,243</td>
<td align="right">74.0%</td>
<td align="right">3,708</td>
<td align="right">24.6%</td>
<td align="right">11,221</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">2,371</td>
<td align="right">15.6%</td>
<td align="right">13,614</td>
<td align="right">89.6%</td>
<td align="right">2,266</td>
<td align="right">15.0%</td>
<td align="right">13,487</td>
<td align="right">89.3%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,588</td>
<td align="right">10.4%</td>
<td align="right">15,202</td>
<td align="right">1,612</td>
<td align="right">10.7%</td>
<td align="right">15,099</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -977,7 +984,7 @@ 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="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4678332</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4679118</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -990,19 +997,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4688237</td>
<td align="center">0.4754386</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4693374</td>
<td align="center">0.4673058</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4641460</td>
<td align="center">0.4625054</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4664644</td>
<td align="center">0.4617169</td>
</tr>
</tbody>
</table>
@ -1020,23 +1027,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4688237</td>
<td align="center">4667</td>
<td align="center">0.4754386</td>
<td align="center">4560</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4693374</td>
<td align="center">5267</td>
<td align="center">0.4673058</td>
<td align="center">5215</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4641460</td>
<td align="center">2301</td>
<td align="center">0.4625054</td>
<td align="center">2307</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4664644</td>
<td align="center">2967</td>
<td align="center">0.4617169</td>
<td align="center">3017</td>
</tr>
</tbody>
</table>
@ -1056,27 +1063,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9249165</td>
<td align="center">0.8956580</td>
<td align="center">0.9929192</td>
<td align="center">0.9237322</td>
<td align="center">0.8957806</td>
<td align="center">0.9952083</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8413098</td>
<td align="center">0.8992443</td>
<td align="center">0.9911839</td>
<td align="center">0.8207196</td>
<td align="center">0.8957816</td>
<td align="center">0.9844913</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9169771</td>
<td align="center">0.9161788</td>
<td align="center">0.9949441</td>
<td align="center">0.9161273</td>
<td align="center">0.9180151</td>
<td align="center">0.9927184</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6280051</td>
<td align="center">0.6160635</td>
<td align="center">0.0000000</td>
<td align="center">0.6280051</td>
<td align="center">0.6160635</td>
</tr>
</tbody>
</table>
@ -1087,36 +1094,36 @@ Longest: 24</p>
<a class="sourceLine" id="cb29-4" title="4"> <span class="st">"2. Gentamicin"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(GEN),</a>
<a class="sourceLine" id="cb29-5" title="5"> <span class="st">"3. Amoxi/clav + genta"</span> =<span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_SI</a></span>(AMC, GEN)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb29-6" title="6"><span class="st"> </span>tidyr<span class="op">::</span><span class="kw"><a href="https://tidyr.tidyverse.org/reference/gather.html">gather</a></span>(<span class="st">"antibiotic"</span>, <span class="st">"S"</span>, <span class="op">-</span>genus) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb29-7" title="7"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> genus,</a>
<a class="sourceLine" id="cb29-7" title="7"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(<span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> genus,</a>
<a class="sourceLine" id="cb29-8" title="8"> <span class="dt">y =</span> S,</a>
<a class="sourceLine" id="cb29-9" title="9"> <span class="dt">fill =</span> antibiotic)) <span class="op">+</span></a>
<a class="sourceLine" id="cb29-10" title="10"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/geom_bar">geom_col</a></span>(<span class="dt">position =</span> <span class="st">"dodge2"</span>)</a></code></pre></div>
<a class="sourceLine" id="cb29-10" title="10"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html">geom_col</a></span>(<span class="dt">position =</span> <span class="st">"dodge2"</span>)</a></code></pre></div>
<p><img src="AMR_files/figure-html/plot%201-1.png" width="720"></p>
</div>
<div id="plots" class="section level2">
<h2 class="hasAnchor">
<a href="#plots" class="anchor"></a>Plots</h2>
<p>To show results in plots, most R users would nowadays use the <code>ggplot2</code> package. This package lets you create plots in layers. You can read more about it <a href="https://ggplot2.tidyverse.org/">on their website</a>. A quick example would look like these syntaxes:</p>
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(<span class="dt">data =</span> a_data_set,</a>
<a class="sourceLine" id="cb30-2" title="2"> <span class="dt">mapping =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> year,</a>
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(<span class="dt">data =</span> a_data_set,</a>
<a class="sourceLine" id="cb30-2" title="2"> <span class="dt">mapping =</span> <span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> year,</a>
<a class="sourceLine" id="cb30-3" title="3"> <span class="dt">y =</span> value)) <span class="op">+</span></a>
<a class="sourceLine" id="cb30-4" title="4"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/geom_bar">geom_col</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb30-5" title="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/labs">labs</a></span>(<span class="dt">title =</span> <span class="st">"A title"</span>,</a>
<a class="sourceLine" id="cb30-4" title="4"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html">geom_col</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb30-5" title="5"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="dt">title =</span> <span class="st">"A title"</span>,</a>
<a class="sourceLine" id="cb30-6" title="6"> <span class="dt">subtitle =</span> <span class="st">"A subtitle"</span>,</a>
<a class="sourceLine" id="cb30-7" title="7"> <span class="dt">x =</span> <span class="st">"My X axis"</span>,</a>
<a class="sourceLine" id="cb30-8" title="8"> <span class="dt">y =</span> <span class="st">"My Y axis"</span>)</a>
<a class="sourceLine" id="cb30-9" title="9"></a>
<a class="sourceLine" id="cb30-10" title="10"><span class="co"># or as short as:</span></a>
<a class="sourceLine" id="cb30-11" title="11"><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(a_data_set) <span class="op">+</span></a>
<a class="sourceLine" id="cb30-12" title="12"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/geom_bar">geom_bar</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(year))</a></code></pre></div>
<a class="sourceLine" id="cb30-11" title="11"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(a_data_set) <span class="op">+</span></a>
<a class="sourceLine" id="cb30-12" title="12"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html">geom_bar</a></span>(<span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(year))</a></code></pre></div>
<p>The <code>AMR</code> package contains functions to extend this <code>ggplot2</code> package, for example <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code>. It automatically transforms data with <code><a href="../reference/count.html">count_df()</a></code> or <code><a href="../reference/portion.html">portion_df()</a></code> and show results in stacked bars. Its simplest and shortest example:</p>
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(data_1st) <span class="op">+</span></a>
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(data_1st) <span class="op">+</span></a>
<a class="sourceLine" id="cb31-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">geom_rsi</a></span>(<span class="dt">translate_ab =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><img src="AMR_files/figure-html/plot%203-1.png" width="720"></p>
<p>Omit the <code>translate_ab = FALSE</code> to have the antibiotic codes (AMX, AMC, CIP, GEN) translated to official WHO names (amoxicillin, amoxicillin/clavulanic acid, ciprofloxacin, gentamicin).</p>
<p>If we group on e.g. the <code>genus</code> column and add some additional functions from our package, we can create this:</p>
<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1"><span class="co"># group the data on `genus`</span></a>
<a class="sourceLine" id="cb32-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(genus)) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb32-2" title="2"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(genus)) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb32-3" title="3"><span class="st"> </span><span class="co"># create bars with genus on x axis</span></a>
<a class="sourceLine" id="cb32-4" title="4"><span class="st"> </span><span class="co"># it looks for variables with class `rsi`,</span></a>
<a class="sourceLine" id="cb32-5" title="5"><span class="st"> </span><span class="co"># of which we have 4 (earlier created with `as.rsi`)</span></a>
@ -1128,13 +1135,13 @@ Longest: 24</p>
<a class="sourceLine" id="cb32-11" title="11"><span class="st"> </span><span class="co"># show percentages on y axis</span></a>
<a class="sourceLine" id="cb32-12" title="12"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">scale_y_percent</a></span>(<span class="dt">breaks =</span> <span class="dv">0</span><span class="op">:</span><span class="dv">4</span> <span class="op">*</span><span class="st"> </span><span class="dv">25</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb32-13" title="13"><span class="st"> </span><span class="co"># turn 90 degrees, to make it bars instead of columns</span></a>
<a class="sourceLine" id="cb32-14" title="14"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/coord_flip">coord_flip</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb32-14" title="14"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/coord_flip.html">coord_flip</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb32-15" title="15"><span class="st"> </span><span class="co"># add labels</span></a>
<a class="sourceLine" id="cb32-16" title="16"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/labs">labs</a></span>(<span class="dt">title =</span> <span class="st">"Resistance per genus and antibiotic"</span>, </a>
<a class="sourceLine" id="cb32-16" title="16"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="dt">title =</span> <span class="st">"Resistance per genus and antibiotic"</span>, </a>
<a class="sourceLine" id="cb32-17" title="17"> <span class="dt">subtitle =</span> <span class="st">"(this is fake data)"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb32-18" title="18"><span class="st"> </span><span class="co"># and print genus in italic to follow our convention</span></a>
<a class="sourceLine" id="cb32-19" title="19"><span class="st"> </span><span class="co"># (is now y axis because we turned the plot)</span></a>
<a class="sourceLine" id="cb32-20" title="20"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/theme">theme</a></span>(<span class="dt">axis.text.y =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/element">element_text</a></span>(<span class="dt">face =</span> <span class="st">"italic"</span>))</a></code></pre></div>
<a class="sourceLine" id="cb32-20" title="20"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/theme.html">theme</a></span>(<span class="dt">axis.text.y =</span> <span class="kw"><a href="https://ggplot2.tidyverse.org/reference/element.html">element_text</a></span>(<span class="dt">face =</span> <span class="st">"italic"</span>))</a></code></pre></div>
<p><img src="AMR_files/figure-html/plot%204-1.png" width="720"></p>
<p>To simplify this, we also created the <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function, which combines almost all above functions:</p>
<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -1143,7 +1150,7 @@ Longest: 24</p>
<a class="sourceLine" id="cb33-4" title="4"> <span class="dt">facet =</span> <span class="st">"antibiotic"</span>,</a>
<a class="sourceLine" id="cb33-5" title="5"> <span class="dt">breaks =</span> <span class="dv">0</span><span class="op">:</span><span class="dv">4</span> <span class="op">*</span><span class="st"> </span><span class="dv">25</span>,</a>
<a class="sourceLine" id="cb33-6" title="6"> <span class="dt">datalabels =</span> <span class="ot">FALSE</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb33-7" title="7"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/coord_flip">coord_flip</a></span>()</a></code></pre></div>
<a class="sourceLine" id="cb33-7" title="7"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/coord_flip.html">coord_flip</a></span>()</a></code></pre></div>
<p><img src="AMR_files/figure-html/plot%205-1.png" width="720"></p>
</div>
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>

2
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>

8
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>
@ -232,9 +232,9 @@
</div>
<div id="amr-0709010" class="section level1">
<div id="amr-0709012" class="section level1">
<h1 class="page-header">
<a href="#amr-0709010" class="anchor"></a>AMR 0.7.0.9010<small> Unreleased </small>
<a href="#amr-0709012" class="anchor"></a>AMR 0.7.0.9012<small> Unreleased </small>
</h1>
<div id="new" class="section level4">
<h4 class="hasAnchor">
@ -1139,7 +1139,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0709010">0.7.0.9010</a></li>
<li><a href="#amr-0709012">0.7.0.9012</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>

4
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>
@ -306,7 +306,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
<p>The function <code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
<p>The function <code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of S, I and R. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
<p>The function <code>rsi_df</code> works exactly like <code>count_df</code>, but add the percentage of S, I and R.</p>
<p>The function <code>rsi_df</code> works exactly like <code>count_df</code>, but adds the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>

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</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">0.7.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>

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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
</span>
</div>
@ -321,7 +321,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. <em>Low counts can infuence the outcome - these <code>portion</code> functions may camouflage this, since they only return the portion albeit being dependent on the <code>minimum</code> parameter.</em></p>
<p>The function <code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each group and each variable with class <code>"rsi"</code>.</p>
<p>The function <code>rsi_df</code> works exactly like <code>portion_df</code>, but add the number of isolates.
<p>The function <code>rsi_df</code> works exactly like <code>portion_df</code>, but adds the number of isolates.
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To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula:
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>