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DESCRIPTION
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Package: AMR
Version: 0.7.1.9002
Version: 0.7.1.9003
Date: 2019-06-23
Title: Antimicrobial Resistance Analysis
Authors@R: c(

6
NEWS.md
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# AMR 0.7.1.9002
# AMR 0.7.1.9003
(no code changes yet)
# AMR 0.7.1
#### 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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 June 2019</h4>
<h4 class="date">23 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 22 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 23 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">2019-06-22</td>
<td align="center">2019-06-23</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">2019-06-22</td>
<td align="center">2019-06-23</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">2019-06-22</td>
<td align="center">2019-06-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,63 +327,30 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-05-06</td>
<td align="center">Y6</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2017-10-01</td>
<td align="center">O3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-10-04</td>
<td align="center">M1</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">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2015-04-19</td>
<td align="center">L8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-08-28</td>
<td align="center">O2</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-04-25</td>
<td align="center">T1</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">2011-03-09</td>
<td align="center">U5</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">2010-05-31</td>
<td align="center">B3</td>
<tr class="odd">
<td align="center">2011-03-26</td>
<td align="center">N5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -392,6 +359,39 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-03-11</td>
<td align="center">O1</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-05-24</td>
<td align="center">V5</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">2016-09-21</td>
<td align="center">Z8</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -411,8 +411,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,382 51.9% 10,382 51.9%
# 2 F 9,618 48.1% 20,000 100.0%</code></pre>
# 1 M 10,366 51.8% 10,366 51.8%
# 2 F 9,634 48.2% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="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 (1,472 new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1,453 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 (1,278 new changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,298 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 (2,802 new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,747 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 (2,239 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (112 new changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,176 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (121 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 6,529 out of 20,000 rows, making a total of 7,903 edits</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,468 out of 20,000 rows, making a total of 7,795 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 7,903 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 117 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,760 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,044 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 324 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,642 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 16 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,795 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 107 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,725 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,040 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 329 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,579 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 15 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 5,683 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,644 first isolates (28.2% of total)</span></a></code></pre></div>
<p>So only 28.2% 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 L1, 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 M3, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -529,19 +529,19 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-06-13</td>
<td align="center">L1</td>
<td align="center">2010-01-24</td>
<td align="center">M3</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">2010-08-25</td>
<td align="center">L1</td>
<td align="center">2010-03-17</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -551,10 +551,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-09-09</td>
<td align="center">L1</td>
<td align="center">2010-04-12</td>
<td align="center">M3</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">R</td>
<td align="center">S</td>
@ -562,63 +562,63 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-14</td>
<td align="center">L1</td>
<td align="center">2010-05-20</td>
<td align="center">M3</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-10-01</td>
<td align="center">L1</td>
<td align="center">2010-06-08</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-15</td>
<td align="center">L1</td>
<td align="center">2010-06-20</td>
<td align="center">M3</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-12-31</td>
<td align="center">L1</td>
<td align="center">2010-09-18</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-01-14</td>
<td align="center">L1</td>
<td align="center">2010-10-08</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-01-31</td>
<td align="center">L1</td>
<td align="center">2010-11-05</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -628,10 +628,10 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-03-23</td>
<td align="center">L1</td>
<td align="center">2010-12-23</td>
<td align="center">M3</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>
@ -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 15,191 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 15,080 first weighted isolates (75.4% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -667,34 +667,34 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-06-13</td>
<td align="center">L1</td>
<td align="center">2010-01-24</td>
<td align="center">M3</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">2010-08-25</td>
<td align="center">L1</td>
<td align="center">2010-03-17</td>
<td align="center">M3</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>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-09-09</td>
<td align="center">L1</td>
<td align="center">2010-04-12</td>
<td align="center">M3</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">R</td>
<td align="center">S</td>
@ -703,35 +703,35 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-14</td>
<td align="center">L1</td>
<td align="center">2010-05-20</td>
<td align="center">M3</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-10-01</td>
<td align="center">L1</td>
<td align="center">2010-06-08</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-15</td>
<td align="center">L1</td>
<td align="center">2010-06-20</td>
<td align="center">M3</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -739,11 +739,11 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-12-31</td>
<td align="center">L1</td>
<td align="center">2010-09-18</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -751,20 +751,20 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-01-14</td>
<td align="center">L1</td>
<td align="center">2010-10-08</td>
<td align="center">M3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-01-31</td>
<td align="center">L1</td>
<td align="center">2010-11-05</td>
<td align="center">M3</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">2011-03-23</td>
<td align="center">L1</td>
<td align="center">2010-12-23</td>
<td align="center">M3</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>
</tbody>
</table>
<p>Instead of 1, now 8 isolates are flagged. In total, 76% of all isolates are marked ‘first weighted’ - 47.5% 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, 75.4% of all isolates are marked ‘first weighted’ - 47.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>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 15,191 isolates for analysis.</p>
<p>So we end up with 15,080 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>
@ -817,47 +817,15 @@
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2014-05-06</td>
<td align="center">Y6</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">2017-10-01</td>
<td align="center">O3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2010-10-04</td>
<td align="center">M1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>3</td>
<td align="center">2015-04-19</td>
<td align="center">L8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">R</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>
@ -865,29 +833,61 @@
</tr>
<tr class="even">
<td>4</td>
<td align="center">2013-08-28</td>
<td align="center">O2</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">R</td>
<td align="center">2013-03-11</td>
<td align="center">O1</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">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>5</td>
<td align="center">2016-05-24</td>
<td align="center">V5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2016-09-21</td>
<td align="center">Z8</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">R</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>7</td>
<td align="center">2012-05-09</td>
<td align="center">B2</td>
<td align="center">Hospital A</td>
<td align="center">2010-09-19</td>
<td align="center">H3</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -897,18 +897,18 @@
</tr>
<tr class="even">
<td>8</td>
<td align="center">2016-11-07</td>
<td align="center">J4</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td align="center">2015-04-27</td>
<td align="center">C9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -928,9 +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> (15,191 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from <code>data_1st</code> (15,080 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,191 (of which NA: 0 = 0.00%)<br>
Length: 15,080 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -947,33 +947,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,443</td>
<td align="right">49.0%</td>
<td align="right">7,443</td>
<td align="right">49.0%</td>
<td align="right">7,414</td>
<td align="right">49.2%</td>
<td align="right">7,414</td>
<td align="right">49.2%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,827</td>
<td align="right">25.2%</td>
<td align="right">11,270</td>
<td align="right">74.2%</td>
<td align="right">3,787</td>
<td align="right">25.1%</td>
<td align="right">11,201</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">2,353</td>
<td align="right">15.5%</td>
<td align="right">13,623</td>
<td align="right">2,319</td>
<td align="right">15.4%</td>
<td align="right">13,520</td>
<td align="right">89.7%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,568</td>
<td align="right">1,560</td>
<td align="right">10.3%</td>
<td align="right">15,191</td>
<td align="right">15,080</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -984,7 +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] 0.4710684</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4661804</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>
@ -997,19 +997,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4769129</td>
<td align="center">0.4658016</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4643125</td>
<td align="center">0.4614653</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4723793</td>
<td align="center">0.4744526</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4731788</td>
<td align="center">0.4686334</td>
</tr>
</tbody>
</table>
@ -1027,23 +1027,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4769129</td>
<td align="center">4548</td>
<td align="center">0.4658016</td>
<td align="center">4547</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4643125</td>
<td align="center">5324</td>
<td align="center">0.4614653</td>
<td align="center">5255</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4723793</td>
<td align="center">2299</td>
<td align="center">0.4744526</td>
<td align="center">2329</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4731788</td>
<td align="center">3020</td>
<td align="center">0.4686334</td>
<td align="center">2949</td>
</tr>
</tbody>
</table>
@ -1063,27 +1063,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9226119</td>
<td align="center">0.8988311</td>
<td align="center">0.9943571</td>
<td align="center">0.9219045</td>
<td align="center">0.8950634</td>
<td align="center">0.9950094</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8010204</td>
<td align="center">0.8903061</td>
<td align="center">0.9795918</td>
<td align="center">0.8153846</td>
<td align="center">0.8935897</td>
<td align="center">0.9865385</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9263130</td>
<td align="center">0.9140319</td>
<td align="center">0.9934675</td>
<td align="center">0.9176129</td>
<td align="center">0.9144442</td>
<td align="center">0.9949828</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6162346</td>
<td align="center">0.6196636</td>
<td align="center">0.0000000</td>
<td align="center">0.6162346</td>
<td align="center">0.6196636</td>
</tr>
</tbody>
</table>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 June 2019</h4>
<h4 class="date">23 June 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

62
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 June 2019</h4>
<h4 class="date">23 June 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -235,19 +235,19 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S S R S R I</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 S S R S R S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R R S S S S</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S I S I S S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 S S I I R R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R R R R R R</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R S R S S S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 I R S S I S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S R R R S R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R S R R I S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 I R R S R S</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 S S S S R R</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 R</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 I</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 I</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 I</span></a></code></pre></div>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 S</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@ -277,40 +277,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,284</td>
<td align="right">65.7%</td>
<td align="right">3,284</td>
<td align="right">65.7%</td>
<td align="right">3,206</td>
<td align="right">64.1%</td>
<td align="right">3,206</td>
<td align="right">64.1%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">675</td>
<td align="right">13.5%</td>
<td align="right">3,959</td>
<td align="right">79.2%</td>
<td align="right">689</td>
<td align="right">13.8%</td>
<td align="right">3,895</td>
<td align="right">77.9%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">570</td>
<td align="right">11.4%</td>
<td align="right">4,529</td>
<td align="right">90.6%</td>
<td align="right">578</td>
<td align="right">11.6%</td>
<td align="right">4,473</td>
<td align="right">89.5%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">263</td>
<td align="right">5.3%</td>
<td align="right">4,792</td>
<td align="right">95.8%</td>
<td align="right">299</td>
<td align="right">6.0%</td>
<td align="right">4,772</td>
<td align="right">95.4%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">208</td>
<td align="right">4.2%</td>
<td align="right">228</td>
<td align="right">4.6%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 June 2019</h4>
<h4 class="date">23 June 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>

4
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 June 2019</h4>
<h4 class="date">23 June 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>

76
docs/articles/benchmarks.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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 June 2019</h4>
<h4 class="date">23 June 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -217,14 +217,14 @@
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18.0 18.0 22 18.0 18.0 63 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 66.0 66.0 71 66.0 66.0 110 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 18.0 18.0 18 18.0 18.0 18 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18.0 18.0 18 18.0 18.0 20 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 53.0 53.0 70 53.0 55.0 180 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 52.0 53.0 73 54.0 97.0 110 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8.2 8.2 17 8.3 8.4 53 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 17.0 18.0 22.0 18.0 18.0 61.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 66.0 66.0 75.0 66.0 68.0 110.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 17.0 18.0 18.0 18.0 18.0 18.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18.0 18.0 32.0 18.0 54.0 80.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 52.0 53.0 57.0 53.0 53.0 96.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 52.0 53.0 78.0 53.0 110.0 150.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8.1 8.1 8.2 8.2 8.2 8.3 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@ -236,12 +236,12 @@
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 400 400 430 430 450 450 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 390 400 420 420 450 460 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 210 210 260 240 270 430 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 210 210 250 260 260 270 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 74 75 94 76 120 120 10</span></a></code></pre></div>
<p>That takes 7 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 390 390 420 440 440 440 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 390 390 420 440 440 450 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 210 250 250 250 260 270 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 210 210 240 220 250 410 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 72 72 82 72 73 120 10</span></a></code></pre></div>
<p>That takes 6.8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
@ -287,8 +287,8 @@
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" title="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1090 1130 1190 1170 1230 1320 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.17 seconds (1167 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1120 1140 1190 1180 1210 1260 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.18 seconds (1182 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -300,11 +300,11 @@
<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 13.00 13.20 13.70 13.60 14.10 14.70 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 50.40 50.90 57.80 51.80 52.80 104.00 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.72 1.77 1.86 1.83 1.98 2.02 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0018 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 12.90 13.1 18.50 13.60 13.90 63.60 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 49.90 50.1 52.20 51.10 52.20 62.60 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.49 1.7 1.76 1.73 1.96 1.98 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0017 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
@ -317,14 +317,14 @@
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" title="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.591 0.635 0.719 0.681 0.808 0.968 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.575 0.643 0.702 0.688 0.738 0.893 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.550 1.660 1.780 1.730 1.920 2.170 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.594 0.685 0.725 0.732 0.760 0.928 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.584 0.614 0.667 0.650 0.730 0.782 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.473 0.479 0.617 0.629 0.712 0.810 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.495 0.526 0.576 0.559 0.602 0.756 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.489 0.519 0.565 0.575 0.607 0.647 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.518 0.544 0.630 0.620 0.683 0.752 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.548 0.650 0.695 0.703 0.728 0.855 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.530 1.600 1.750 1.780 1.880 1.950 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.541 0.640 0.690 0.665 0.728 0.857 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.496 0.545 0.610 0.612 0.680 0.754 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.523 0.547 0.613 0.580 0.701 0.756 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.528 0.547 0.586 0.568 0.600 0.743 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.547 0.553 0.634 0.609 0.670 0.864 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -351,13 +351,13 @@
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 43.75 43.82 44.07 43.93 44.28 44.90 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 45.96 46.09 47.68 46.20 46.65 59.40 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 59.57 59.72 64.49 59.88 60.34 104.30 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 45.82 45.89 50.72 46.30 46.60 90.94 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 45.77 45.94 55.86 46.46 48.05 96.85 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 45.67 45.99 55.17 46.39 46.78 92.03 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 45.84 45.92 46.27 46.04 46.36 47.24 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 43.34 43.72 43.76 43.82 43.93 43.98 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 45.77 45.82 46.40 45.90 46.21 50.16 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 59.12 59.39 60.61 59.81 60.97 65.36 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 45.35 45.70 55.58 46.30 50.91 90.30 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 45.54 45.72 47.36 46.02 46.23 57.97 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 45.44 45.68 55.49 45.91 46.30 97.86 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 45.60 45.68 52.57 45.79 46.17 110.10 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 June 2019</h4>
<h4 class="date">23 June 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>

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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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
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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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>
@ -232,9 +232,15 @@
</div>
<div id="amr-0719002" class="section level1">
<div id="amr-0719003" class="section level1">
<h1 class="page-header">
<a href="#amr-0719002" class="anchor"></a>AMR 0.7.1.9002<small> Unreleased </small>
<a href="#amr-0719003" class="anchor"></a>AMR 0.7.1.9003<small> Unreleased </small>
</h1>
<p>(no code changes yet)</p>
</div>
<div id="amr-071" class="section level1">
<h1 class="page-header">
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
</h1>
<div id="new" class="section level4">
<h4 class="hasAnchor">
@ -1141,7 +1147,8 @@ 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-0719002">0.7.1.9002</a></li>
<li><a href="#amr-0719003">0.7.1.9003</a></li>
<li><a href="#amr-071">0.7.1</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>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

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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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/microorganisms.codes.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/microorganisms.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/microorganisms.old.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/mo_property.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/mo_source.html
View File

@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/p.symbol.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/portion.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/read.4D.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/resistance_predict.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/rsi_translation.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/septic_patients.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/skewness.html
View File

@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

2
docs/reference/translate.html
View File

@ -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">0.7.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
</span>
</div>

28
git_siteonly.sh
View File

@ -6,32 +6,12 @@
# bash git_merge.sh #
#######################################################################
echo "•••••••••••••••••••••"
echo "• Reloading package •"
echo "•••••••••••••••••••••"
Rscript -e "devtools::load_all()"
Rscript -e "devtools::document()"
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
echo
echo "•••••••••••••••••"
echo "• Building site •"
echo "•••••••••••••••••"
Rscript -e "suppressMessages(pkgdown::build_site(lazy = TRUE, examples = FALSE))"
bash git_premaster.sh "website update" FALSE
echo
read -p "Continue (Y/n)? " choice
case "$choice" in
n|N ) exit 1;;
* ) ;;
esac
echo
echo "•••••••••••••••••••••••••••"
echo "• Uploading to repository •"
echo "•••••••••••••••••••••••••••"
git add .
git commit -a -m "website update" --quiet
# git push --quiet
echo "••••••••••••••••••••••••••••••"
echo "• Uploading to master branch •"
echo "••••••••••••••••••••••••••••••"
git checkout master
git merge premaster
git push --quiet