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Author SHA1 Message Date
dr. M.S. (Matthijs) Berends
41d279daa1 (v1.7.0) v1.7.0 2021-05-26 11:10:34 +02:00
dr. M.S. (Matthijs) Berends
a12572c752 doc update 2021-05-26 11:00:32 +02:00
dr. M.S. (Matthijs) Berends
a33c8a51a2 v1.7.0 2021-05-26 10:59:54 +02:00
21 changed files with 302 additions and 296 deletions
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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.0
Date: 2021-05-24
Date: 2021-05-26
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),

4
R/resistance_predict.R
View File

@ -98,8 +98,10 @@
#' model = "binomial",
#' info = FALSE,
#' minimum = 15)
#'
#' ggplot(data)
#'
#' ggplot(data,
#' ggplot(as.data.frame(data),
#' aes(x = year)) +
#' geom_col(aes(y = value),
#' fill = "grey75") +

BIN
data-raw/AMR_latest.tar.gz
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Binary file not shown.

556
docs/articles/AMR.html
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@ -193,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">24 May 2021</h4>
<h4 class="date">26 May 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -202,7 +202,7 @@
<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 24 May 2021.</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 26 May 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-05-24</td>
<td align="center">2021-05-26</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">2021-05-24</td>
<td align="center">2021-05-26</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">2021-05-24</td>
<td align="center">2021-05-26</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -344,70 +344,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-04-11</td>
<td align="center">W8</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</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">2013-06-11</td>
<td align="center">I7</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2013-01-28</td>
<td align="center">G4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-12-30</td>
<td align="center">C6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-03-16</td>
<td align="center">P5</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-03-27</td>
<td align="center">U2</td>
<td align="center">2014-08-13</td>
<td align="center">O10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-10-06</td>
<td align="center">N1</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">M</td>
</tr>
<tr class="even">
<td align="center">2016-08-07</td>
<td align="center">J6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</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">2010-06-21</td>
<td align="center">Q4</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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">2011-01-31</td>
<td align="center">E5</td>
<td align="center">Hospital B</td>
<td align="center">2016-04-25</td>
<td align="center">R4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -424,7 +424,7 @@
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 20,000<br>
Available: 20,000 (100%, NA: 0 = 0%)<br>
Available: 20,000 (100.0%, NA: 0 = 0.0%)<br>
Unique: 2</p>
<p>Shortest: 1<br>
Longest: 1</p>
@ -441,16 +441,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,485</td>
<td align="right">52.43%</td>
<td align="right">10,485</td>
<td align="right">52.43%</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,515</td>
<td align="right">47.58%</td>
<td align="right">9,597</td>
<td align="right">47.99%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -505,9 +505,9 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,696 first weighted isolates (phenotype-based, 53.5% of total</span>
<span class="co"># =&gt; Found 10,682 first weighted isolates (phenotype-based, 53.4% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 53.5% 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>
<p>So only 53.4% 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="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -515,7 +515,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,696 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,682 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table class="table">
@ -553,45 +553,13 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">6</td>
<td align="center">2011-01-31</td>
<td align="center">E5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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 align="left">8</td>
<td align="center">2016-02-04</td>
<td align="center">A9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</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">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2015-07-09</td>
<td align="center">N1</td>
<td align="center">Hospital B</td>
<td align="left">4</td>
<td align="center">2016-08-07</td>
<td align="center">J6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -601,30 +569,46 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2013-11-10</td>
<td align="center">M10</td>
<td align="center">Hospital B</td>
<td align="left">6</td>
<td align="center">2016-04-25</td>
<td align="center">R4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">12</td>
<td align="center">2013-12-10</td>
<td align="center">W8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="left">10</td>
<td align="center">2016-01-17</td>
<td align="center">R3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="left">11</td>
<td align="center">2013-01-18</td>
<td align="center">S1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@ -632,20 +616,36 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">15</td>
<td align="center">2016-11-20</td>
<td align="center">U2</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<tr class="odd">
<td align="left">16</td>
<td align="center">2017-07-05</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">19</td>
<td align="center">2013-10-30</td>
<td align="center">D4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -669,8 +669,8 @@ Longest: 1</p>
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,696<br>
Available: 10,696 (100%, NA: 0 = 0%)<br>
Length: 10,682<br>
Available: 10,682 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -687,33 +687,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,648</td>
<td align="right">43.46%</td>
<td align="right">4,648</td>
<td align="right">43.46%</td>
<td align="right">4,559</td>
<td align="right">42.68%</td>
<td align="right">4,559</td>
<td align="right">42.68%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,729</td>
<td align="right">25.51%</td>
<td align="right">7,377</td>
<td align="right">68.97%</td>
<td align="right">2,844</td>
<td align="right">26.62%</td>
<td align="right">7,403</td>
<td align="right">69.30%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,136</td>
<td align="right">19.97%</td>
<td align="right">9,513</td>
<td align="right">88.94%</td>
<td align="right">2,082</td>
<td align="right">19.49%</td>
<td align="right">9,485</td>
<td align="right">88.79%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,183</td>
<td align="right">11.06%</td>
<td align="right">10,696</td>
<td align="right">1,197</td>
<td align="right">11.21%</td>
<td align="right">10,682</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -760,89 +760,89 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-02-04</td>
<td align="center">A9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-07-09</td>
<td align="center">N1</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</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="odd">
<td align="center">2017-06-21</td>
<td align="center">M8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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 align="center">2010-09-28</td>
<td align="center">V7</td>
<td align="center">2016-08-07</td>
<td align="center">J6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="odd">
<td align="center">2012-08-30</td>
<td align="center">N9</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-08-23</td>
<td align="center">I4</td>
<td align="center">2016-01-17</td>
<td align="center">R3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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="odd">
<td align="center">2017-07-05</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2013-10-30</td>
<td align="center">D4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-02-20</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-02-18</td>
<td align="center">F5</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
@ -870,50 +870,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2236</td>
<td align="center">124</td>
<td align="center">2288</td>
<td align="center">4648</td>
<td align="center">2129</td>
<td align="center">151</td>
<td align="center">2279</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3462</td>
<td align="center">154</td>
<td align="center">1032</td>
<td align="center">4648</td>
<td align="center">3355</td>
<td align="center">151</td>
<td align="center">1053</td>
<td align="center">4559</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3400</td>
<td align="center">3320</td>
<td align="center">0</td>
<td align="center">1248</td>
<td align="center">4648</td>
<td align="center">1239</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4040</td>
<td align="center">3995</td>
<td align="center">0</td>
<td align="center">608</td>
<td align="center">4648</td>
<td align="center">564</td>
<td align="center">4559</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1183</td>
<td align="center">1183</td>
<td align="center">1197</td>
<td align="center">1197</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">937</td>
<td align="center">48</td>
<td align="center">198</td>
<td align="center">1183</td>
<td align="center">949</td>
<td align="center">46</td>
<td align="center">202</td>
<td align="center">1197</td>
</tr>
</tbody>
</table>
@ -936,34 +936,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4040</td>
<td align="center">3995</td>
<td align="center">0</td>
<td align="center">608</td>
<td align="center">4648</td>
<td align="center">564</td>
<td align="center">4559</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1066</td>
<td align="center">1077</td>
<td align="center">0</td>
<td align="center">117</td>
<td align="center">1183</td>
<td align="center">120</td>
<td align="center">1197</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2418</td>
<td align="center">2523</td>
<td align="center">0</td>
<td align="center">311</td>
<td align="center">2729</td>
<td align="center">321</td>
<td align="center">2844</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2136</td>
<td align="center">2136</td>
<td align="center">2082</td>
<td align="center">2082</td>
</tr>
</tbody>
</table>
@ -977,7 +977,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
<span class="co"># [1] 0.5431002</span></code></pre></div>
<span class="co"># [1] 0.5449354</span></code></pre></div>
<p>Or can be used in conjunction 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="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -991,19 +991,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5389075</td>
<td align="center">0.5437286</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5612520</td>
<td align="center">0.5478284</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5325596</td>
<td align="center">0.5407268</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5259019</td>
<td align="center">0.5448113</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5389075</td>
<td align="center">3277</td>
<td align="center">0.5437286</td>
<td align="center">3213</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5612520</td>
<td align="center">3706</td>
<td align="center">0.5478284</td>
<td align="center">3753</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5325596</td>
<td align="center">1551</td>
<td align="center">0.5407268</td>
<td align="center">1596</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5259019</td>
<td align="center">2162</td>
<td align="center">0.5448113</td>
<td align="center">2120</td>
</tr>
</tbody>
</table>
@ -1059,27 +1059,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7779690</td>
<td align="center">0.8691910</td>
<td align="center">0.9733219</td>
<td align="center">0.7690283</td>
<td align="center">0.8762887</td>
<td align="center">0.9782847</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8326289</td>
<td align="center">0.9010989</td>
<td align="center">0.9805579</td>
<td align="center">0.8312448</td>
<td align="center">0.8997494</td>
<td align="center">0.9874687</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7933309</td>
<td align="center">0.8860388</td>
<td align="center">0.9805790</td>
<td align="center">0.7960619</td>
<td align="center">0.8871308</td>
<td align="center">0.9820675</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5397940</td>
<td align="center">0.5249760</td>
<td align="center">0.0000000</td>
<td align="center">0.5397940</td>
<td align="center">0.5249760</td>
</tr>
</tbody>
</table>
@ -1163,19 +1163,19 @@ Longest: 24</p>
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] &gt;=128 &lt;=0.0625 64 4 0.25 16 8 2 </span>
<span class="co"># [9] 0.25 &gt;=128 0.25 &gt;=128 0.25 0.5 64 0.125 </span>
<span class="co"># [17] 2 &lt;=0.0625 0.5 2 1 0.5 32 &gt;=128 </span>
<span class="co"># [25] 0.5 32 &gt;=128 0.25 &lt;=0.0625 &lt;=0.0625 0.5 2 </span>
<span class="co"># [33] &gt;=128 &gt;=128 4 8 &lt;=0.0625 &lt;=0.0625 4 16 </span>
<span class="co"># [41] &gt;=128 32 &lt;=0.0625 &gt;=128 1 &lt;=0.0625 0.5 8 </span>
<span class="co"># [49] 0.125 4 &lt;=0.0625 16 4 32 0.125 8 </span>
<span class="co"># [57] 4 4 16 4 &gt;=128 &lt;=0.0625 4 32 </span>
<span class="co"># [65] 0.125 64 0.5 0.125 0.5 4 16 32 </span>
<span class="co"># [73] 0.125 0.25 4 0.25 4 &gt;=128 &gt;=128 16 </span>
<span class="co"># [81] 1 &lt;=0.0625 0.125 1 4 4 &lt;=0.0625 0.125 </span>
<span class="co"># [89] 0.125 &gt;=128 16 2 0.25 64 8 16 </span>
<span class="co"># [97] 4 &gt;=128 8 &gt;=128</span></code></pre></div>
<span class="co"># [1] 4 &lt;=0.0625 64 0.5 0.5 0.125 128 128 </span>
<span class="co"># [9] 0.5 &lt;=0.0625 4 32 256 0.25 64 8 </span>
<span class="co"># [17] 32 64 4 2 1 4 16 128 </span>
<span class="co"># [25] 128 32 &lt;=0.0625 32 2 4 16 0.125 </span>
<span class="co"># [33] 0.25 0.5 32 128 64 128 0.125 256 </span>
<span class="co"># [41] 1 &lt;=0.0625 64 1 0.25 0.5 &lt;=0.0625 64 </span>
<span class="co"># [49] 8 1 4 2 32 &lt;=0.0625 &lt;=0.0625 4 </span>
<span class="co"># [57] 128 4 32 128 128 32 0.25 64 </span>
<span class="co"># [65] 16 0.5 4 0.5 0.25 4 &lt;=0.0625 2 </span>
<span class="co"># [73] 0.125 0.5 256 &lt;=0.0625 0.5 1 256 0.25 </span>
<span class="co"># [81] 64 64 8 256 16 256 64 16 </span>
<span class="co"># [89] 128 0.125 8 &lt;=0.0625 4 16 128 128 </span>
<span class="co"># [97] 16 128 0.5 1</span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@ -1204,10 +1204,10 @@ Longest: 24</p>
<span class="co"># to review it.</span>
<span class="va">disk_values</span>
<span class="co"># Class &lt;disk&gt;</span>
<span class="co"># [1] 21 24 22 27 19 23 24 30 27 27 30 22 26 21 29 18 31 31 17 20 24 28 21 20 25</span>
<span class="co"># [26] 21 17 19 26 28 21 17 30 27 25 30 30 22 21 25 21 19 17 19 28 25 24 27 23 27</span>
<span class="co"># [51] 26 21 17 18 26 19 31 27 27 25 28 24 20 17 24 21 26 26 26 22 27 27 22 19 23</span>
<span class="co"># [76] 17 27 22 17 26 30 31 28 27 19 23 24 31 22 28 31 27 31 23 29 19 18 30 27 28</span></code></pre></div>
<span class="co"># [1] 22 19 28 26 29 31 30 27 29 17 20 21 19 28 28 24 30 31 17 26 19 30 31 29 24</span>
<span class="co"># [26] 18 22 25 26 25 26 21 25 25 21 29 29 22 30 25 30 28 29 29 21 20 22 18 20 25</span>
<span class="co"># [51] 25 21 27 31 26 17 23 28 21 22 24 25 30 18 26 24 22 22 18 31 20 21 25 22 26</span>
<span class="co"># [76] 31 30 23 18 31 20 24 21 28 31 18 24 27 28 30 28 29 29 22 28 30 30 25 24 31</span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>

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docs/articles/datasets.html
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@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">24 May 2021</h4>
<h4 class="date">26 May 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>

8
docs/index.html
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@ -376,11 +376,11 @@
<div id="latest-released-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
<p><a href="https://cran.r-project.org/package=AMR"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
<p>This package is available on the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, as CRAN does not allow frequent updates of large packages. With CRAN, we cannot update this package frequently enough to implement the latest EUCAST/CLSI guidelines or the latest microbial taxonomy.</p>
<p>Install this package in R by using the command:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></code></pre></div>
<p>It will be downloaded and installed automatically.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
<div id="latest-development-version" class="section level4">

2
docs/news/index.html
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@ -456,7 +456,7 @@
<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
</li>
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>

4
docs/pkgdown.yml
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@ -1,4 +1,4 @@
pandoc: 2.11.2
pandoc: 2.11.4
pkgdown: 1.6.1
pkgdown_sha: ~
articles:
@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-24T12:27Z
last_built: 2021-05-26T09:09Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

6
docs/reference/resistance_predict.html
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@ -276,7 +276,7 @@
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ggplot</span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
<span class='va'>x</span>,
@ -432,8 +432,10 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
model <span class='op'>=</span> <span class='st'>"binomial"</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
minimum <span class='op'>=</span> <span class='fl'>15</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>data</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='va'>year</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span><span class='op'>(</span><span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>y <span class='op'>=</span> <span class='va'>value</span><span class='op'>)</span>,
fill <span class='op'>=</span> <span class='st'>"grey75"</span><span class='op'>)</span> <span class='op'>+</span>

10
index.md
View File

@ -97,16 +97,16 @@ This package can be used for:
### Get this package
#### Latest released version
[![CRAN](https://www.r-pkg.org/badges/version-ago/AMR)](https://cran.r-project.org/package=AMR)
[![CRANlogs](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://cran.r-project.org/package=AMR)
This package is available [here on the official R network (CRAN)](https://cran.r-project.org/package=AMR), which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:
This package is available on the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), as CRAN does not allow frequent updates of large packages. With CRAN, we cannot update this package frequently enough to implement the latest EUCAST/CLSI guidelines or the latest microbial taxonomy.
Install this package in R by using the command:
```r
install.packages("AMR")
install.packages("AMR", repos = "https://msberends.r-universe.dev")
```
It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
It will be downloaded and installed automatically.
**Note:** Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.

4
man/resistance_predict.Rd
View File

@ -165,8 +165,10 @@ if (require("dplyr") & require("ggplot2")) {
model = "binomial",
info = FALSE,
minimum = 15)
ggplot(data)
ggplot(data,
ggplot(as.data.frame(data),
aes(x = year)) +
geom_col(aes(y = value),
fill = "grey75") +