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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.6.1.9051
Version: 0.6.1.9052
Date: 2019-06-01
Title: Antimicrobial Resistance Analysis
Authors@R: c(

8
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.6.1.90xx
# AMR 0.6.1.9052
**Note: latest development version**
#### New
@ -17,7 +17,8 @@
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
* All `atc_*` functions are superceded by `ab_*` functions
* All output will be translated by using an included translation file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv)
* All output will be translated by using an included translation file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv).
Please [create an issue in one of our repositories](https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion) if you want additions in this file.
* Improvements to plotting AMR results with `ggplot_rsi()`:
* New parameter `colours` to set the bar colours
@ -41,7 +42,8 @@
freq(age) %>%
boxplot()
```
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv)
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv).
Please [create an issue in one of our repositories](https://gitlab.com/msberends/AMR/issues/new?issue[title]=EUCAST%20edit) if you want changes in this file.
* Added ceftazidim intrinsic resistance to *Streptococci*
* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+

2
_pkgdown.yml
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@ -23,6 +23,8 @@ title: 'AMR (for R)'
url: 'https://msberends.gitlab.io/AMR'
development:
mode: release # improves indexing by search engines
# version_label: default
version_tooltip: "Latest development version"
news:
one_page: true

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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="Released version">0.6.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -208,7 +208,7 @@
<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 31 May 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 01 June 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -224,21 +224,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-05-31</td>
<td align="center">2019-06-01</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">2019-05-31</td>
<td align="center">2019-06-01</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">2019-05-31</td>
<td align="center">2019-06-01</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -334,8 +334,8 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-03-08</td>
<td align="center">Q4</td>
<td align="center">2011-01-05</td>
<td align="center">W4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -345,19 +345,8 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-12-18</td>
<td align="center">J6</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="odd">
<td align="center">2016-07-07</td>
<td align="center">W7</td>
<td align="center">2013-05-10</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
@ -366,9 +355,9 @@
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-12-08</td>
<td align="center">G9</td>
<tr class="odd">
<td align="center">2011-07-24</td>
<td align="center">L6</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
@ -377,27 +366,38 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-09-08</td>
<td align="center">Y8</td>
<tr class="even">
<td align="center">2017-12-18</td>
<td align="center">P2</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-03-27</td>
<td align="center">I8</td>
<td align="center">Hospital D</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">M</td>
</tr>
<tr class="even">
<td align="center">2017-05-04</td>
<td align="center">X10</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">2013-05-25</td>
<td align="center">L4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</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>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -418,8 +418,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,387 51.9% 10,387 51.9%
# 2 F 9,613 48.1% 20,000 100.0%</code></pre>
# 1 M 10,472 52.4% 10,472 52.4%
# 2 F 9,528 47.6% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher 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>
@ -449,14 +449,14 @@
<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 (1533 new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1519 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 (1285 new changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1280 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 (2841 new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2810 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>
@ -464,24 +464,24 @@
<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 (2277 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (127 new changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2266 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (95 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 6,664 out of 20,000 rows, making a total of 8,063 edits</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,560 out of 20,000 rows, making a total of 7,970 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 8,063 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 121 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,826 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,112 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 355 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,622 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 27 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,970 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 118 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,807 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,119 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 318 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,590 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 18 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-54" 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>
@ -509,8 +509,8 @@
<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 5,672 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 5,704 first isolates (28.5% of total)</span></a></code></pre></div>
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" 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>
@ -536,8 +536,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-20</td>
<td align="center">P7</td>
<td align="center">2010-01-23</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -547,8 +547,8 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-28</td>
<td align="center">P7</td>
<td align="center">2010-03-03</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -558,41 +558,41 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-09</td>
<td align="center">P7</td>
<td align="center">2010-03-26</td>
<td align="center">H6</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>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-04-23</td>
<td align="center">P7</td>
<td align="center">2010-04-21</td>
<td align="center">H6</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-07</td>
<td align="center">P7</td>
<td align="center">2010-07-15</td>
<td align="center">H6</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">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">2010-05-15</td>
<td align="center">P7</td>
<td align="center">2010-08-13</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -602,10 +602,10 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-07-16</td>
<td align="center">P7</td>
<td align="center">2010-09-29</td>
<td align="center">H6</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>
@ -613,8 +613,8 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-07-31</td>
<td align="center">P7</td>
<td align="center">2010-10-10</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -624,24 +624,24 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-10</td>
<td align="center">P7</td>
<td align="center">2010-12-09</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-09</td>
<td align="center">P7</td>
<td align="center">2010-12-11</td>
<td align="center">H6</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>
</tbody>
@ -657,7 +657,7 @@
<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 15,152 first weighted isolates (75.8% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,183 first weighted isolates (75.9% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -674,8 +674,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-20</td>
<td align="center">P7</td>
<td align="center">2010-01-23</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -686,8 +686,8 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-28</td>
<td align="center">P7</td>
<td align="center">2010-03-03</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -698,23 +698,23 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-09</td>
<td align="center">P7</td>
<td align="center">2010-03-26</td>
<td align="center">H6</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>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-04-23</td>
<td align="center">P7</td>
<td align="center">2010-04-21</td>
<td align="center">H6</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -722,20 +722,8 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-05-07</td>
<td align="center">P7</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">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-05-15</td>
<td align="center">P7</td>
<td align="center">2010-07-15</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -744,12 +732,24 @@
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-13</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-07-16</td>
<td align="center">P7</td>
<td align="center">2010-09-29</td>
<td align="center">H6</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>
@ -758,8 +758,8 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-07-31</td>
<td align="center">P7</td>
<td align="center">2010-10-10</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -770,11 +770,11 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-10</td>
<td align="center">P7</td>
<td align="center">2010-12-09</td>
<td align="center">H6</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -782,23 +782,23 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-09</td>
<td align="center">P7</td>
<td align="center">2010-12-11</td>
<td align="center">H6</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>
</tr>
</tbody>
</table>
<p>Instead of 1, now 9 isolates are flagged. In total, 75.8% of all isolates are marked ‘first weighted’ - 47.4% 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 9 isolates are flagged. In total, 75.9% of all isolates are marked ‘first weighted’ - 47.4% 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 15,152 isolates for analysis.</p>
<p>So we end up with 15,183 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>
@ -806,6 +806,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -822,8 +823,9 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-03-08</td>
<td align="center">Q4</td>
<td>1</td>
<td align="center">2011-01-05</td>
<td align="center">W4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
@ -837,23 +839,9 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-12-18</td>
<td align="center">J6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-07-07</td>
<td align="center">W7</td>
<td>2</td>
<td align="center">2013-05-10</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
@ -866,13 +854,30 @@
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-12-08</td>
<td align="center">G9</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AUR</td>
<tr class="odd">
<td>4</td>
<td align="center">2017-12-18</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2013-05-25</td>
<td align="center">L4</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</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>
@ -882,30 +887,32 @@
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-09-08</td>
<td align="center">Y8</td>
<td>7</td>
<td align="center">2016-09-17</td>
<td align="center">F3</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>8</td>
<td align="center">2010-06-30</td>
<td align="center">L8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-05-04</td>
<td align="center">X10</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">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -928,9 +935,9 @@
<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 a <code>data.frame</code> (15,152 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,183 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,152 (of which NA: 0 = 0.00%)<br>
Length: 15,183 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -947,33 +954,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,455</td>
<td align="right">49.2%</td>
<td align="right">7,455</td>
<td align="right">49.2%</td>
<td align="right">7,416</td>
<td align="right">48.8%</td>
<td align="right">7,416</td>
<td align="right">48.8%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,759</td>
<td align="right">24.8%</td>
<td align="right">11,214</td>
<td align="right">74.0%</td>
<td align="right">3,781</td>
<td align="right">24.9%</td>
<td align="right">11,197</td>
<td align="right">73.7%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,398</td>
<td align="right">15.8%</td>
<td align="right">13,612</td>
<td align="right">89.8%</td>
<td align="right">2,391</td>
<td align="right">15.7%</td>
<td align="right">13,588</td>
<td align="right">89.5%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,540</td>
<td align="right">10.2%</td>
<td align="right">15,152</td>
<td align="right">1,595</td>
<td align="right">10.5%</td>
<td align="right">15,183</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -984,7 +991,7 @@ 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] 0.467727</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4716459</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 +1004,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4577496</td>
<td align="center">0.4789879</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4703985</td>
<td align="center">0.4752328</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4736842</td>
<td align="center">0.4525453</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4736322</td>
<td align="center">0.4688136</td>
</tr>
</tbody>
</table>
@ -1027,23 +1034,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4577496</td>
<td align="center">4568</td>
<td align="center">0.4789879</td>
<td align="center">4545</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4703985</td>
<td align="center">5270</td>
<td align="center">0.4752328</td>
<td align="center">5370</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4736842</td>
<td align="center">2280</td>
<td align="center">0.4525453</td>
<td align="center">2318</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4736322</td>
<td align="center">3034</td>
<td align="center">0.4688136</td>
<td align="center">2950</td>
</tr>
</tbody>
</table>
@ -1063,27 +1070,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9238095</td>
<td align="center">0.8940309</td>
<td align="center">0.9919517</td>
<td align="center">0.9224649</td>
<td align="center">0.8938781</td>
<td align="center">0.9920442</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8285714</td>
<td align="center">0.9038961</td>
<td align="center">0.9883117</td>
<td align="center">0.8119122</td>
<td align="center">0.9072100</td>
<td align="center">0.9874608</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9199255</td>
<td align="center">0.9159351</td>
<td align="center">0.9938814</td>
<td align="center">0.9185401</td>
<td align="center">0.9098122</td>
<td align="center">0.9920656</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6192661</td>
<td align="center">0.6056043</td>
<td align="center">0.0000000</td>
<td align="center">0.6192661</td>
<td align="center">0.6056043</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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

4
docs/articles/G_test.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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>G_test.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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -242,19 +242,19 @@
<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 R R S R R S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 I S R R I I</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S I R R R R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S R S R R S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 S S I S S S</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R R S S R S</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S R S S R S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 S S I R R R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S S R R I S</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S S R R S R</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 S R R R R R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R R S S S I</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 I</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 S</span></a>
<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="cb3-10" title="10"><span class="co"># 1 R</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 I</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</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 R</span></a></code></pre></div>
<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>
@ -285,39 +285,39 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,232</td>
<td align="right">64.6%</td>
<td align="right">3,232</td>
<td align="right">64.6%</td>
<td align="right">3,300</td>
<td align="right">66.0%</td>
<td align="right">3,300</td>
<td align="right">66.0%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">693</td>
<td align="right">13.9%</td>
<td align="right">3,925</td>
<td align="right">78.5%</td>
<td align="right">649</td>
<td align="right">13.0%</td>
<td align="right">3,949</td>
<td align="right">79.0%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">603</td>
<td align="right">12.1%</td>
<td align="right">4,528</td>
<td align="right">90.6%</td>
<td align="right">586</td>
<td align="right">11.7%</td>
<td align="right">4,535</td>
<td align="right">90.7%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">276</td>
<td align="right">5.5%</td>
<td align="right">4,804</td>
<td align="right">270</td>
<td align="right">5.4%</td>
<td align="right">4,805</td>
<td align="right">96.1%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">196</td>
<td align="right">195</td>
<td align="right">3.9%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 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="Released version">0.6.1.9044</span>
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</span>
</div>
@ -199,7 +199,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>WHONET.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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>ab_property.Rmd</code></div>

70
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -225,13 +225,13 @@
<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") 17 18 24 18 18 78.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 48 48 52 48 48 92.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 18 18 27 18 18 62.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18 18 18 18 18 18.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 28 29 46 29 73 73.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 28 29 42 29 29 110.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8 8 8 8 8 8.1 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 17.0 18 37 18 62.0 80.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 48.0 48 52 48 48.0 92.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 18.0 18 31 18 62.0 66.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 17.0 18 18 18 18.0 18.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 28.0 28 37 28 29.0 110.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 28.0 29 33 29 29.0 72.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 7.9 8 8 8 8.1 8.1 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>
@ -243,12 +243,12 @@
<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") 470 470 500 520 520 520 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 470 470 500 500 520 520 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 74 74 79 75 76 120 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 74 74 90 74 120 140 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 73 73 83 74 76 120 10</span></a></code></pre></div>
<p>That takes 8.1 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") 470 470 480 470 480 510 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 470 470 500 520 520 530 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 74 74 93 75 120 130 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 74 74 94 78 120 120 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 73 73 83 73 75 130 10</span></a></code></pre></div>
<p>That takes 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>
@ -294,8 +294,8 @@
<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) 725 767 825 792 903 944 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.79 seconds (791 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) 636 664 728 716 763 880 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.72 seconds (715 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -308,9 +308,9 @@
<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 13.20 13.30 17.90 13.40 13.40 58.30 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 25.60 25.80 26.00 26.00 26.20 26.50 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.62 1.81 1.78 1.81 1.82 1.86 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 13.3 13.30 18.10 13.50 14.20 57.90 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 25.7 25.80 26.50 26.20 27.50 27.50 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.6 1.82 1.86 1.84 2.02 2.07 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>
<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>
@ -324,14 +324,14 @@
<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 0.517 0.550 0.608 0.588 0.637 0.839 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.540 0.548 0.666 0.679 0.744 0.829 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.690 1.790 1.880 1.860 1.990 2.050 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.588 0.632 0.704 0.694 0.731 0.944 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.487 0.504 0.629 0.614 0.703 0.920 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.477 0.540 0.587 0.579 0.640 0.754 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.505 0.550 0.628 0.605 0.755 0.768 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.189 0.266 0.294 0.297 0.362 0.379 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.483 0.579 0.616 0.615 0.654 0.729 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.578 0.657 0.680 0.671 0.680 0.834 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.550 1.640 1.840 1.920 1.980 2.100 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.562 0.746 0.796 0.782 0.847 1.010 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.502 0.578 0.641 0.601 0.755 0.786 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.482 0.553 0.613 0.614 0.684 0.751 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.540 0.560 0.586 0.571 0.604 0.672 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.216 0.272 0.301 0.296 0.352 0.380 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">
@ -358,13 +358,13 @@
<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 18.45 18.51 18.69 18.72 18.78 19.01 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 23.32 23.41 23.67 23.45 24.00 24.41 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 36.79 36.88 41.71 37.39 37.57 81.66 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 23.32 23.39 23.75 23.65 23.93 24.82 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 23.31 23.33 33.07 23.38 29.77 69.13 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 23.33 23.38 27.93 23.43 23.55 67.91 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 23.35 23.38 28.12 23.47 23.82 67.82 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 18.43 18.46 23.22 18.61 18.81 64.60 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 20.89 20.99 25.96 21.39 22.23 66.53 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 34.35 34.46 34.62 34.55 34.68 35.22 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 20.88 20.92 21.31 21.06 21.58 22.21 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 20.59 20.85 20.94 20.93 21.14 21.22 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 20.85 21.09 21.15 21.13 21.23 21.58 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 20.95 21.22 25.92 21.44 21.61 66.66 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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -275,16 +275,17 @@ Longest: 1</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/base/topics/colnames">colnames</a></span>(microorganisms)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># [1] "mo" "col_id" "fullname" "kingdom" "phylum" </span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># [6] "class" "order" "family" "genus" "species" </span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subspecies" "rank" "ref" "species_id" "source"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:</p>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subspecies" "rank" "ref" "species_id" "source" </span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># [16] "prevalence"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 15 variables were added:</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/base/topics/dim">dim</a></span>(septic_patients)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># [1] 2000 49</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_patients)</a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 63</span></a></code></pre></div>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 64</span></a></code></pre></div>
<p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">my_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 63)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 64)</strong></p>
<p>Columns: 2<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 95</p>

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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="Released version">0.6.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>mo_property.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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 May 2019</h4>
<h4 class="date">01 June 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>

2
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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="Released version">0.6.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

4
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@ -17,7 +17,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
*/
@ -138,7 +138,9 @@ help {
/* hide version label */
.version.label {
/*
display: none;
*/
}
/* Date of vignettes */

2
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

18
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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="Released version">0.6.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>
@ -239,9 +239,9 @@
</div>
<div id="amr-06190xx" class="section level1">
<div id="amr-0619052" class="section level1">
<h1 class="page-header">
<a href="#amr-06190xx" class="anchor"></a>AMR 0.6.1.90xx<small> Unreleased </small>
<a href="#amr-0619052" class="anchor"></a>AMR 0.6.1.9052<small> Unreleased </small>
</h1>
<p><strong>Note: latest development version</strong></p>
<div id="new" class="section level4">
@ -272,7 +272,9 @@
<li>All references to antibiotics in our package now use EARS-Net codes, like <code>AMX</code> for amoxicillin</li>
<li>Functions <code>atc_certe</code>, <code>ab_umcg</code> and <code>atc_trivial_nl</code> have been removed</li>
<li>All <code>atc_*</code> functions are superceded by <code>ab_*</code> functions</li>
<li>All output will be translated by using an included translation file which <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv">can be viewed here</a> Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Translation%20suggestion">create an issue in one of our repositories</a> if you want additions in this file.</li>
<li>
<p>All output will be translated by using an included translation file which <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv">can be viewed here</a>.</p>
Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Translation%20suggestion">create an issue in one of our repositories</a> if you want additions in this file.</li>
</ul>
</li>
<li>Improvements to plotting AMR results with <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>:
@ -305,7 +307,9 @@
</li>
</ul>
</li>
<li>Removed all hardcoded EUCAST rules and replaced them with a new reference file which <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv">can be viewed here</a> Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUCAST%20edit">create an issue in one of our repositories</a> if you want changes in this file.</li>
<li>
<p>Removed all hardcoded EUCAST rules and replaced them with a new reference file which <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv">can be viewed here</a>.</p>
Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUCAST%20edit">create an issue in one of our repositories</a> if you want changes in this file.</li>
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
@ -318,7 +322,7 @@
<li>Small algorithm fix for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Removed viruses from data set <code>microorganisms.codes</code> and cleaned it up</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</li>
<li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
</ul>
</div>
<div id="other" class="section level4">
@ -1061,7 +1065,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-06190xx">0.6.1.90</a></li>
<li><a href="#amr-0619052">0.6.1.9052</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>
<li><a href="#amr-050">0.5.0</a></li>

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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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/filter_ab_class.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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/first_isolate.html
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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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/freq.html
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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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/g.test.html
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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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
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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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/index.html
View File

@ -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="Released version">0.6.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/join.html
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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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/key_antibiotics.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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/kurtosis.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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/like.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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

2
docs/reference/mdro.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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</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="Released version">0.6.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span>
</span>
</div>

5
git_premaster.sh
View File

@ -27,9 +27,14 @@ current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
# combine tag (e.g. 0.1.0) and commit number (like 40) increased by 9000 to indicate beta version
new_version="$current_tag.$((current_commit + 9000))" # results in 0.1.0.9040
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
# update 1st line of NEWS.md
sed -i -- "1s/${current_tag}.*/${new_version}/" NEWS.md
echo "First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION
echo
echo "First line of NEWS.md:"
head -1 NEWS.md
echo
echo "•••••••••••••••••••••••••••••••••"
echo "• Reloading/documenting package •"
echo "•••••••••••••••••••••••••••••••••"

4
pkgdown/extra.css
View File

@ -17,7 +17,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
*/
@ -138,7 +138,9 @@ help {
/* hide version label */
.version.label {
/*
display: none;
*/
}
/* Date of vignettes */