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dr. M.S. (Matthijs) Berends 2019-06-02 19:50:22 +02:00
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_pkgdown.yml
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@ -23,8 +23,6 @@ title: 'AMR (for R)'
url: 'https://msberends.gitlab.io/AMR' url: 'https://msberends.gitlab.io/AMR'
development: development:
mode: release # improves indexing by search engines mode: release # improves indexing by search engines
# version_label: default
version_tooltip: "Latest development version"
news: news:
one_page: true one_page: true

452
docs/articles/AMR.html
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@ -334,42 +334,31 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2014-06-27</td> <td align="center">2014-12-18</td>
<td align="center">V8</td> <td align="center">S8</td>
<td align="center">Hospital B</td> <td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</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">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2013-02-12</td> <td align="center">2010-05-29</td>
<td align="center">L4</td> <td align="center">Z4</td>
<td align="center">Hospital A</td> <td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td> <td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">S</td>
<td align="center">F</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2013-11-26</td> <td align="center">2015-11-20</td>
<td align="center">T2</td> <td align="center">G6</td>
<td align="center">Hospital A</td> <td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-12-27</td>
<td align="center">J10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</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>
@ -377,28 +366,39 @@
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
</tr> </tr>
<tr class="odd">
<td align="center">2013-09-22</td>
<td align="center">I7</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even"> <tr class="even">
<td align="center">2014-01-26</td> <td align="center">2015-11-07</td>
<td align="center">Q6</td> <td align="center">Q10</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
</tr> </tr>
<tr class="odd">
<td align="center">2013-11-26</td>
<td align="center">P8</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-30</td>
<td align="center">L3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody> </tbody>
</table> </table>
<p>Now, let’s start the cleaning and the analysis!</p> <p>Now, let’s start the cleaning and the analysis!</p>
@ -418,8 +418,8 @@
# #
# Item Count Percent Cum. Count Cum. Percent # Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- ------------- # --- ----- ------- -------- ----------- -------------
# 1 M 10,233 51.2% 10,233 51.2% # 1 M 10,420 52.1% 10,420 52.1%
# 2 F 9,767 48.8% 20,000 100.0%</code></pre> # 2 F 9,580 47.9% 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>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> <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> <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="cb14-18" 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="cb14-19" 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="cb14-20" 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 (1509 new changes)</span></a> <a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1421 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="cb14-22" 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="cb14-23" 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="cb14-24" 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 (1276 new changes)</span></a> <a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1367 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="cb14-26" 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="cb14-27" 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 (2758 new changes)</span></a> <a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2632 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="cb14-29" 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="cb14-30" 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> <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="cb14-33" 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="cb14-34" 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="cb14-35" 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 (2254 new changes)</span></a> <a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2233 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (138 new changes)</span></a> <a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (113 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="cb14-38" 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="cb14-39" 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="cb14-40" 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="cb14-41" 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="cb14-42" title="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co"># --------------------------------------------------------------------------</span></a> <a class="sourceLine" id="cb14-43" title="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,564 out of 20,000 rows, making a total of 7,935 edits</span></a> <a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,458 out of 20,000 rows, making a total of 7,766 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="cb14-45" 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="cb14-46" title="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,935 test results</span></a> <a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,766 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 109 test results changed from S to I</span></a> <a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 106 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,768 test results changed from S to R</span></a> <a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,695 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,081 test results changed from I to S</span></a> <a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,068 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 345 test results changed from I to R</span></a> <a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 323 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,615 test results changed from R to S</span></a> <a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,556 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 17 test results changed from R to I</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="cb14-54" title="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-55" title="55"><span class="co"># </span></a> <a class="sourceLine" id="cb14-55" 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> <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>
@ -509,7 +509,7 @@
<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="cb16-3" 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="cb16-4" 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="cb16-5" 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 5,664 first isolates (28.3% of total)</span></a></code></pre></div> <a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,665 first isolates (28.3% of total)</span></a></code></pre></div>
<p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p> <p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<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> <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> <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>
@ -536,8 +536,8 @@
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">1</td> <td align="center">1</td>
<td align="center">2010-01-07</td> <td align="center">2010-01-18</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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>
@ -547,43 +547,43 @@
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2</td> <td align="center">2</td>
<td align="center">2010-02-14</td> <td align="center">2010-01-26</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">3</td> <td align="center">3</td>
<td align="center">2010-02-18</td> <td align="center">2010-02-26</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">4</td> <td align="center">4</td>
<td align="center">2010-06-01</td> <td align="center">2010-03-13</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">5</td> <td align="center">5</td>
<td align="center">2010-08-14</td> <td align="center">2010-08-18</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -591,8 +591,8 @@
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">6</td> <td align="center">6</td>
<td align="center">2010-11-08</td> <td align="center">2010-12-10</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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>
@ -602,21 +602,21 @@
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">7</td> <td align="center">7</td>
<td align="center">2010-11-16</td> <td align="center">2011-05-02</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">8</td> <td align="center">8</td>
<td align="center">2010-12-11</td> <td align="center">2011-05-02</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -624,22 +624,22 @@
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">9</td> <td align="center">9</td>
<td align="center">2011-02-27</td> <td align="center">2011-05-15</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">TRUE</td> <td align="center">S</td>
<td align="center">FALSE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">10</td> <td align="center">10</td>
<td align="center">2011-03-06</td> <td align="center">2011-05-15</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">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>
@ -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="cb19-7" 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="cb19-8" 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="cb19-9" 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 15,014 first weighted isolates (75.1% of total)</span></a></code></pre></div> <a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,064 first weighted isolates (75.3% of total)</span></a></code></pre></div>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
<th align="center">isolate</th> <th align="center">isolate</th>
@ -674,8 +674,8 @@
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">1</td> <td align="center">1</td>
<td align="center">2010-01-07</td> <td align="center">2010-01-18</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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>
@ -686,46 +686,46 @@
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2</td> <td align="center">2</td>
<td align="center">2010-02-14</td> <td align="center">2010-01-26</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">3</td> <td align="center">3</td>
<td align="center">2010-02-18</td> <td align="center">2010-02-26</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">4</td> <td align="center">4</td>
<td align="center">2010-06-01</td> <td align="center">2010-03-13</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">5</td> <td align="center">5</td>
<td align="center">2010-08-14</td> <td align="center">2010-08-18</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -734,8 +734,8 @@
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">6</td> <td align="center">6</td>
<td align="center">2010-11-08</td> <td align="center">2010-12-10</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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>
@ -746,47 +746,47 @@
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">7</td> <td align="center">7</td>
<td align="center">2010-11-16</td> <td align="center">2011-05-02</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</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">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">8</td> <td align="center">8</td>
<td align="center">2010-12-11</td> <td align="center">2011-05-02</td>
<td align="center">K9</td> <td align="center">T2</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">9</td>
<td align="center">2011-02-27</td>
<td align="center">K9</td>
<td align="center">B_ESCHR_COL</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">S</td> <td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-05-15</td>
<td align="center">T2</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">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">10</td> <td align="center">10</td>
<td align="center">2011-03-06</td> <td align="center">2011-05-15</td>
<td align="center">K9</td> <td align="center">T2</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">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>
@ -794,11 +794,11 @@
</tr> </tr>
</tbody> </tbody>
</table> </table>
<p>Instead of 2, now 9 isolates are flagged. In total, 75.1% of all isolates are marked ‘first weighted’ - 46.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p> <p>Instead of 2, now 9 isolates are flagged. In total, 75.3% of all isolates are marked ‘first weighted’ - 47% 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> <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> <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> <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 15,014 isolates for analysis.</p> <p>So we end up with 15,064 isolates for analysis.</p>
<p>We can remove unneeded columns:</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> <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> <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>
@ -823,93 +823,93 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td>1</td> <td>3</td>
<td align="center">2014-06-27</td> <td align="center">2015-11-20</td>
<td align="center">V8</td> <td align="center">G6</td>
<td align="center">Hospital B</td> <td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNE</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>4</td>
<td align="center">2015-11-07</td>
<td align="center">Q10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">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">F</td>
<td align="center">Gram negative</td> <td align="center">Gram negative</td>
<td align="center">Klebsiella</td> <td align="center">Escherichia</td>
<td align="center">pneumoniae</td> <td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="odd">
<td>2</td> <td>5</td>
<td align="center">2013-02-12</td> <td align="center">2013-11-26</td>
<td align="center">L4</td> <td align="center">P8</td>
<td align="center">Hospital A</td> <td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td> <td align="center">B_STRPT_PNE</td>
<td align="center">I</td> <td align="center">S</td>
<td align="center">I</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">M</td> <td align="center">F</td>
<td align="center">Gram positive</td> <td align="center">Gram positive</td>
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">pneumoniae</td> <td align="center">pneumoniae</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd">
<td>3</td>
<td align="center">2013-11-26</td>
<td align="center">T2</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even"> <tr class="even">
<td>5</td> <td>6</td>
<td align="center">2013-09-22</td> <td align="center">2014-07-30</td>
<td align="center">I7</td> <td align="center">L3</td>
<td align="center">Hospital C</td> <td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
<td align="center">Gram positive</td> <td align="center">Gram negative</td>
<td align="center">Staphylococcus</td> <td align="center">Escherichia</td>
<td align="center">aureus</td> <td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td>7</td> <td>7</td>
<td align="center">2012-03-30</td> <td align="center">2016-04-08</td>
<td align="center">L8</td> <td align="center">C7</td>
<td align="center">Hospital B</td> <td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
<td align="center">Gram positive</td> <td align="center">Gram negative</td>
<td align="center">Staphylococcus</td> <td align="center">Escherichia</td>
<td align="center">aureus</td> <td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td>8</td> <td>8</td>
<td align="center">2015-08-27</td> <td align="center">2010-02-28</td>
<td align="center">L4</td> <td align="center">A8</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
@ -935,9 +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> <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> <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> <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> (15,014 x 13)</strong></p> <p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,064 x 13)</strong></p>
<p>Columns: 2<br> <p>Columns: 2<br>
Length: 15,014 (of which NA: 0 = 0.00%)<br> Length: 15,064 (of which NA: 0 = 0.00%)<br>
Unique: 4</p> Unique: 4</p>
<p>Shortest: 16<br> <p>Shortest: 16<br>
Longest: 24</p> Longest: 24</p>
@ -954,33 +954,33 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Escherichia coli</td> <td align="left">Escherichia coli</td>
<td align="right">7,496</td> <td align="right">7,474</td>
<td align="right">49.9%</td> <td align="right">49.6%</td>
<td align="right">7,496</td> <td align="right">7,474</td>
<td align="right">49.9%</td> <td align="right">49.6%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Staphylococcus aureus</td> <td align="left">Staphylococcus aureus</td>
<td align="right">3,663</td> <td align="right">3,691</td>
<td align="right">24.4%</td> <td align="right">24.5%</td>
<td align="right">11,159</td> <td align="right">11,165</td>
<td align="right">74.3%</td> <td align="right">74.1%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td> <td align="left">Streptococcus pneumoniae</td>
<td align="right">2,303</td> <td align="right">2,238</td>
<td align="right">15.3%</td> <td align="right">14.9%</td>
<td align="right">13,462</td> <td align="right">13,403</td>
<td align="right">89.7%</td> <td align="right">89.0%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td> <td align="left">Klebsiella pneumoniae</td>
<td align="right">1,552</td> <td align="right">1,661</td>
<td align="right">10.3%</td> <td align="right">11.0%</td>
<td align="right">15,014</td> <td align="right">15,064</td>
<td align="right">100.0%</td> <td align="right">100.0%</td>
</tr> </tr>
</tbody> </tbody>
@ -991,7 +991,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2> <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> <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> <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] 0.4708938</span></a></code></pre></div> <a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4719862</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> <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> <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> <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>
@ -1004,19 +1004,19 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.4625681</td> <td align="center">0.4641785</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.4799232</td> <td align="center">0.4697084</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.4727660</td> <td align="center">0.4838129</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.4660767</td> <td align="center">0.4796271</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1034,23 +1034,23 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.4625681</td> <td align="center">0.4641785</td>
<td align="center">4408</td> <td align="center">4662</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.4799232</td> <td align="center">0.4697084</td>
<td align="center">5205</td> <td align="center">5282</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.4727660</td> <td align="center">0.4838129</td>
<td align="center">2350</td> <td align="center">2224</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.4660767</td> <td align="center">0.4796271</td>
<td align="center">3051</td> <td align="center">2896</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1070,27 +1070,27 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Escherichia</td> <td align="center">Escherichia</td>
<td align="center">0.9252935</td> <td align="center">0.9211935</td>
<td align="center">0.8992796</td> <td align="center">0.8898849</td>
<td align="center">0.9945304</td> <td align="center">0.9933101</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Klebsiella</td> <td align="center">Klebsiella</td>
<td align="center">0.8150773</td> <td align="center">0.8169777</td>
<td align="center">0.9059278</td> <td align="center">0.8832029</td>
<td align="center">0.9864691</td> <td align="center">0.9843468</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">0.9216489</td> <td align="center">0.9184503</td>
<td align="center">0.9211029</td> <td align="center">0.9170956</td>
<td align="center">0.9923560</td> <td align="center">0.9937686</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">0.6026921</td> <td align="center">0.6090259</td>
<td align="center">0.0000000</td> <td align="center">0.0000000</td>
<td align="center">0.6026921</td> <td align="center">0.6090259</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>

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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to apply EUCAST rules</h1> <h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div> <div class="hidden name"><code>EUCAST.Rmd</code></div>

4
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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to use the <em>G</em>-test</h1> <h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>G_test.Rmd</code></div> <div class="hidden name"><code>G_test.Rmd</code></div>

62
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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1> <h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div> <div class="hidden name"><code>MDR.Rmd</code></div>
@ -242,18 +242,18 @@
<p>The data set looks like this now:</p> <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> <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="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S R S S R S</span></a> <a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S R R S S 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="cb3-4" title="4"><span class="co"># 2 S I S S R S</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="cb3-5" title="5"><span class="co"># 3 S I S S S 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="cb3-6" title="6"><span class="co"># 4 S I S 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="cb3-7" title="7"><span class="co"># 5 I S S S S 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="cb3-8" title="8"><span class="co"># 6 S S R S R I</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a> <a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 R</span></a> <a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 I</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</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 I</span></a> <a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</span></a> <a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 S</span></a> <a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 I</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 S</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> <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">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a> <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
@ -285,40 +285,40 @@ Unique: 5</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Mono-resistance</td> <td align="left">Mono-resistance</td>
<td align="right">3,300</td> <td align="right">3,249</td>
<td align="right">66.0%</td> <td align="right">65.0%</td>
<td align="right">3,300</td> <td align="right">3,249</td>
<td align="right">66.0%</td> <td align="right">65.0%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Negative</td> <td align="left">Negative</td>
<td align="right">649</td> <td align="right">670</td>
<td align="right">13.0%</td> <td align="right">13.4%</td>
<td align="right">3,949</td> <td align="right">3,919</td>
<td align="right">79.0%</td> <td align="right">78.4%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Multidrug resistance</td> <td align="left">Multidrug resistance</td>
<td align="right">586</td> <td align="right">604</td>
<td align="right">11.7%</td> <td align="right">12.1%</td>
<td align="right">4,535</td> <td align="right">4,523</td>
<td align="right">90.7%</td> <td align="right">90.5%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Poly-resistance</td> <td align="left">Poly-resistance</td>
<td align="right">270</td> <td align="right">289</td>
<td align="right">5.4%</td> <td align="right">5.8%</td>
<td align="right">4,805</td> <td align="right">4,812</td>
<td align="right">96.1%</td> <td align="right">96.2%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">5</td>
<td align="left">Extensive drug resistance</td> <td align="left">Extensive drug resistance</td>
<td align="right">195</td> <td align="right">188</td>
<td align="right">3.9%</td> <td align="right">3.8%</td>
<td align="right">5,000</td> <td align="right">5,000</td>
<td align="right">100.0%</td> <td align="right">100.0%</td>
</tr> </tr>

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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1> <h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div> <div class="hidden name"><code>SPSS.Rmd</code></div>

4
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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to work with WHONET data</h1> <h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div> <div class="hidden name"><code>WHONET.Rmd</code></div>

4
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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to get properties of an antibiotic</h1> <h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>ab_property.Rmd</code></div> <div class="hidden name"><code>ab_property.Rmd</code></div>

78
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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>Benchmarks</h1> <h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div> <div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -224,14 +224,14 @@
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a> <a class="sourceLine" id="cb2-9" 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="cb2-10" 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="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 17.0 18 37 18 62.0 80.0 10</span></a> <a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18 18 27.0 18 18.0 62.0 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="cb2-13" title="13"><span class="co"># as.mo("stau") 48 48 48.0 48 48.0 48.0 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="cb2-14" title="14"><span class="co"># as.mo("staaur") 18 18 27.0 18 18.0 63.0 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="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18 18 28.0 18 18.0 81.0 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="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 28 28 33.0 29 29.0 73.0 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="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 28 29 47.0 30 72.0 110.0 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> <a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8 8 8.1 8 8.1 8.2 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>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> <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> <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="cb3-7" 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="cb3-8" 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="cb3-9" 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") 470 470 480 470 480 510 10</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") 470 470 500 520 520 530 10</span></a> <a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 470 470 500 500 520 530 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="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 74 74 86 74 76 140 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="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 74 74 80 76 77 120 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> <a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 73 73 89 74 120 140 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>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>
<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> <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> <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> <a class="sourceLine" id="cb4-2" title="2"></a>
@ -293,9 +293,9 @@
<a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<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="cb5-24" 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="cb5-25" 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="cb5-26" 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) 636 664 728 716 763 880 10</span></a></code></pre></div> <a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1080 1120 1160 1130 1180 1340 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> <p>So transforming 500,000 values (!!) of 50 unique values only takes 1.13 seconds (1128 ms). You only lose time on your unique input values.</p>
</div> </div>
<div id="precalculated-results" class="section level3"> <div id="precalculated-results" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -307,11 +307,11 @@
<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a> <a class="sourceLine" id="cb6-5" 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="cb6-6" 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="cb6-7" 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 13.3 13.30 18.10 13.50 14.20 57.90 10</span></a> <a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 13.10 13.5 13.70 13.60 13.70 14.70 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="cb6-9" title="9"><span class="co"># B 25.70 25.9 31.10 27.00 27.70 70.30 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> <a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.61 1.8 1.87 1.85 1.95 2.05 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> <p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 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> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a> <a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a> <a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
@ -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="cb7-10" 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="cb7-11" 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="cb7-12" 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 0.483 0.579 0.616 0.615 0.654 0.729 10</span></a> <a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.495 0.521 0.626 0.631 0.723 0.822 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="cb7-14" title="14"><span class="co"># B 0.581 0.652 0.710 0.716 0.760 0.841 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="cb7-15" title="15"><span class="co"># C 1.520 1.610 1.810 1.780 1.940 2.220 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="cb7-16" title="16"><span class="co"># D 0.617 0.655 0.742 0.724 0.798 0.973 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="cb7-17" title="17"><span class="co"># E 0.506 0.573 0.648 0.615 0.707 0.902 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="cb7-18" title="18"><span class="co"># F 0.515 0.555 0.621 0.589 0.638 0.868 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="cb7-19" title="19"><span class="co"># G 0.512 0.572 0.633 0.608 0.713 0.805 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> <a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.191 0.284 0.303 0.303 0.334 0.397 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> <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>
<div id="results-in-other-languages" class="section level3"> <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="cb8-18" 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="cb8-19" 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="cb8-20" 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 18.43 18.46 23.22 18.61 18.81 64.60 10</span></a> <a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 18.44 18.47 18.68 18.57 18.79 19.33 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="cb8-22" title="22"><span class="co"># de 21.04 21.07 21.27 21.15 21.26 21.85 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="cb8-23" title="23"><span class="co"># nl 34.34 34.55 34.70 34.67 34.87 35.06 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="cb8-24" title="24"><span class="co"># es 20.91 21.01 30.28 21.28 21.55 67.00 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="cb8-25" title="25"><span class="co"># it 20.80 20.98 25.89 21.46 21.86 66.53 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="cb8-26" title="26"><span class="co"># fr 20.93 21.08 21.12 21.11 21.13 21.42 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> <a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 20.94 21.03 25.81 21.40 21.64 66.15 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p> <p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div> </div>
</div> </div>

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docs/articles/freq.html
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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to create frequency tables</h1> <h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div> <div class="hidden name"><code>freq.Rmd</code></div>

4
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@ -40,7 +40,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>
@ -199,7 +199,7 @@
<h1>How to get properties of a microorganism</h1> <h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 June 2019</h4> <h4 class="date">02 June 2019</h4>
<div class="hidden name"><code>mo_property.Rmd</code></div> <div class="hidden name"><code>mo_property.Rmd</code></div>

6
docs/extra.css
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@ -136,11 +136,8 @@ help {
font-size: 1.5em; font-size: 1.5em;
} }
/* hide version label */
.version.label { .version.label {
/*
display: none; display: none;
*/
} }
/* Date of vignettes */ /* Date of vignettes */
@ -215,6 +212,3 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
white-space: normal; white-space: normal;
} }
#search-input {
max-width: 100px;
}

15
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@ -21,19 +21,20 @@
# ==================================================================== # # ==================================================================== #
*/ */
// Add updated Font Awesome 5.6.3 library // Add updated Font Awesome 5.8.2 library
$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">'); $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.2/css/all.css">');
// Add Disqus // Add Disqus
// $('head').append('<link rel="preload" href="https://amr-for-r.disqus.com/embed.js" as="script">');
$('head').append('<script src="https://amr-for-r.disqus.com/embed.js" data-timestamp="' + new Date() + '"></script>'); $('head').append('<script src="https://amr-for-r.disqus.com/embed.js" data-timestamp="' + new Date() + '"></script>');
// Email template for new GitLab issues // Email template for new GitLab issues
//https://stackoverflow.com/a/33190494/4575331 //https://stackoverflow.com/a/33190494/4575331
//incoming+msberends-amr-9011429-5miwzuo1xo70wbz9r6fwv4dmg-issue@incoming.gitlab.com //incoming+msberends-amr-9011429-5miwzuo1xo70wbz9r6fwv4dmg-issue@incoming.gitlab.com
// Edit footer
$( document ).ready(function() { $( document ).ready(function() {
// remove version label from header
$(".version.label").remove();
// redirect to GitLab // redirect to GitLab
var url_old = window.location.href; var url_old = window.location.href;
var url_new = url_old.replace("github", "gitlab"); var url_new = url_old.replace("github", "gitlab");
@ -41,8 +42,8 @@ $( document ).ready(function() {
window.location.replace(url_new); window.location.replace(url_new);
} }
// PR for 'R for Data Science' on How To pages
if ($(".template-article").length > 0) { if ($(".template-article").length > 0) {
// PR for 'R for Data Science' on How To pages
$('#sidebar').prepend( $('#sidebar').prepend(
'<div id="r4ds">' + '<div id="r4ds">' +
' <a target="_blank" href="https://r4ds.had.co.nz/">' + ' <a target="_blank" href="https://r4ds.had.co.nz/">' +
@ -55,7 +56,7 @@ $( document ).ready(function() {
'</div>'); '</div>');
} }
// Add Disqus to all pages // add Disqus to all pages
var disqus = var disqus =
'<button id="btn_collapseDisqus" class="btn btn-primary" type="button" data-toggle="collapse" data-target="#collapseDisqus" aria-expanded="false" aria-controls="collapseDisqus">' + '<button id="btn_collapseDisqus" class="btn btn-primary" type="button" data-toggle="collapse" data-target="#collapseDisqus" aria-expanded="false" aria-controls="collapseDisqus">' +
' Having a question? Or knowing something we don\'t? Click here to open comments.' + ' Having a question? Or knowing something we don\'t? Click here to open comments.' +
@ -67,7 +68,7 @@ $( document ).ready(function() {
$(disqus).insertBefore('footer'); $(disqus).insertBefore('footer');
$('#disqus_thread footer').remove(); $('#disqus_thread footer').remove();
// Alter footer // edit footer
$('footer').html( $('footer').html(
'<div>' + '<div>' +
'<p>' + $('footer .copyright p').html().replace( '<p>' + $('footer .copyright p').html().replace(

2
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/WHONET.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/ab_property.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/age.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/age_groups.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/antibiotics.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/as.ab.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/as.atc.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/as.disk.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/as.mic.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/as.mo.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/as.rsi.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/atc_online.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/availability.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/catalogue_of_life_version.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/count.html
View File

@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/filter_ab_class.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/first_isolate.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </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> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/g.test.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/guess_ab_col.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/join.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/key_antibiotics.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/kurtosis.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/like.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

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docs/reference/mdro.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

12
docs/reference/microorganisms.html
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@ -252,7 +252,17 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An object of class <code>data.frame</code> with 67903 rows and 16 columns.</p> <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,903 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
<dt><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code></dt><dd><p>Taxonomic rank of the microorganism</p></dd>
<dt><code>rank</code></dt><dd><p>Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
<dt><code>species_id</code></dt><dd><p>ID of the species as used by the Catalogue of Life</p></dd>
<dt><code>source</code></dt><dd><p>Either <code>"CoL"</code>, <code>"DSMZ"</code> (see source) or "manually added"</p></dd>
<dt><code>prevalence</code></dt><dd><p>Prevalence of the microorganism, see <code><a href='as.mo.html'>?as.mo</a></code></p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

2
docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/mo_property.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/mo_source.html
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@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/p.symbol.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/portion.html
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/read.4D.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/resistance_predict.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/rsi_translation.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/septic_patients.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/skewness.html
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@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
docs/reference/translate.html
View File

@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9052</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span> </span>
</div> </div>

2
git_merge.sh
View File

@ -10,6 +10,8 @@
# git stash --quiet # git stash --quiet
# go to master # go to master
git add .
git commit -a -m "website update" --quiet
git checkout master --quiet git checkout master --quiet
echo "changed branch to master" echo "changed branch to master"
# import everything from premaster # import everything from premaster

13
man/microorganisms.Rd
View File

@ -4,7 +4,18 @@
\name{microorganisms} \name{microorganisms}
\alias{microorganisms} \alias{microorganisms}
\title{Data set with ~65,000 microorganisms} \title{Data set with ~65,000 microorganisms}
\format{An object of class \code{data.frame} with 67903 rows and 16 columns.} \format{A \code{\link{data.frame}} with 67,903 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{fullname}}{Full name, like \code{"Escherichia coli"}}
\item{\code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}}{Taxonomic rank of the microorganism}
\item{\code{rank}}{Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
\item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
\item{\code{source}}{Either \code{"CoL"}, \code{"DSMZ"} (see source) or "manually added"}
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
}}
\source{ \source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}). Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).

6
pkgdown/extra.css
View File

@ -136,11 +136,8 @@ help {
font-size: 1.5em; font-size: 1.5em;
} }
/* hide version label */
.version.label { .version.label {
/*
display: none; display: none;
*/
} }
/* Date of vignettes */ /* Date of vignettes */
@ -215,6 +212,3 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
white-space: normal; white-space: normal;
} }
#search-input {
max-width: 100px;
}

15
pkgdown/extra.js
View File

@ -21,19 +21,20 @@
# ==================================================================== # # ==================================================================== #
*/ */
// Add updated Font Awesome 5.6.3 library // Add updated Font Awesome 5.8.2 library
$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">'); $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.2/css/all.css">');
// Add Disqus // Add Disqus
// $('head').append('<link rel="preload" href="https://amr-for-r.disqus.com/embed.js" as="script">');
$('head').append('<script src="https://amr-for-r.disqus.com/embed.js" data-timestamp="' + new Date() + '"></script>'); $('head').append('<script src="https://amr-for-r.disqus.com/embed.js" data-timestamp="' + new Date() + '"></script>');
// Email template for new GitLab issues // Email template for new GitLab issues
//https://stackoverflow.com/a/33190494/4575331 //https://stackoverflow.com/a/33190494/4575331
//incoming+msberends-amr-9011429-5miwzuo1xo70wbz9r6fwv4dmg-issue@incoming.gitlab.com //incoming+msberends-amr-9011429-5miwzuo1xo70wbz9r6fwv4dmg-issue@incoming.gitlab.com
// Edit footer
$( document ).ready(function() { $( document ).ready(function() {
// remove version label from header
$(".version.label").remove();
// redirect to GitLab // redirect to GitLab
var url_old = window.location.href; var url_old = window.location.href;
var url_new = url_old.replace("github", "gitlab"); var url_new = url_old.replace("github", "gitlab");
@ -41,8 +42,8 @@ $( document ).ready(function() {
window.location.replace(url_new); window.location.replace(url_new);
} }
// PR for 'R for Data Science' on How To pages
if ($(".template-article").length > 0) { if ($(".template-article").length > 0) {
// PR for 'R for Data Science' on How To pages
$('#sidebar').prepend( $('#sidebar').prepend(
'<div id="r4ds">' + '<div id="r4ds">' +
' <a target="_blank" href="https://r4ds.had.co.nz/">' + ' <a target="_blank" href="https://r4ds.had.co.nz/">' +
@ -55,7 +56,7 @@ $( document ).ready(function() {
'</div>'); '</div>');
} }
// Add Disqus to all pages // add Disqus to all pages
var disqus = var disqus =
'<button id="btn_collapseDisqus" class="btn btn-primary" type="button" data-toggle="collapse" data-target="#collapseDisqus" aria-expanded="false" aria-controls="collapseDisqus">' + '<button id="btn_collapseDisqus" class="btn btn-primary" type="button" data-toggle="collapse" data-target="#collapseDisqus" aria-expanded="false" aria-controls="collapseDisqus">' +
' Having a question? Or knowing something we don\'t? Click here to open comments.' + ' Having a question? Or knowing something we don\'t? Click here to open comments.' +
@ -67,7 +68,7 @@ $( document ).ready(function() {
$(disqus).insertBefore('footer'); $(disqus).insertBefore('footer');
$('#disqus_thread footer').remove(); $('#disqus_thread footer').remove();
// Alter footer // edit footer
$('footer').html( $('footer').html(
'<div>' + '<div>' +
'<p>' + $('footer .copyright p').html().replace( '<p>' + $('footer .copyright p').html().replace(