P281424/AMR
1
0 Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-10-01 04:13:33 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9059@e7d7b94

Browse Source
This commit is contained in:
github-actions committed 2022-12-09 14:17:23 +00:00
1 parent 09ffdc91e6
commit 4dff2dbe6b
97 files changed
+482 -479
Download Patch File Download Diff File Expand all files Collapse all files

No files matched your search

404.html
+1 -1
View File
@@ -36,7 +36,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
LICENSE-text.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/AMR.html
+229 -227
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -400,67 +400,67 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-03-05</td>
<td align="center">N7</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-11-26</td>
<td align="center">A7</td>
<td align="center">2015-07-01</td>
<td align="center">N10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-06-30</td>
<td align="center">X1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</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">F</td>
</tr>
<tr class="even">
<td align="center">2011-06-27</td>
<td align="center">O7</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-09-14</td>
<td align="center">I4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-08-07</td>
<td align="center">R7</td>
<td align="center">2017-06-08</td>
<td align="center">T6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-05-17</td>
<td align="center">Q7</td>
<td align="center">Hospital D</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">2013-01-27</td>
<td align="center">T4</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-06-25</td>
<td align="center">X6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-10-09</td>
<td align="center">U7</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella 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>
@@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,429</td>
<td align="right">52.15%</td>
<td align="right">10,429</td>
<td align="right">52.15%</td>
<td align="right">10,352</td>
<td align="right">51.76%</td>
<td align="right">10,352</td>
<td align="right">51.76%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,571</td>
<td align="right">47.86%</td>
<td align="right">9,648</td>
<td align="right">48.24%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,584 'phenotype-based' first isolates (52.9% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,610 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 52.9% is suitable for resistance analysis! We can now filter
<p>So only 53.1% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,584 isolates for analysis. Now our data looks
<p>So we end up with 10,610 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
@@ -674,13 +674,13 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-03-05</td>
<td align="center">N7</td>
<td align="center">Hospital D</td>
<td align="center">2015-07-01</td>
<td align="center">N10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@@ -689,10 +689,10 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2011-06-27</td>
<td align="center">O7</td>
<td align="center">Hospital B</td>
<td align="left">2</td>
<td align="center">2017-06-08</td>
<td align="center">T6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@@ -705,30 +705,30 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2016-09-14</td>
<td align="center">I4</td>
<td align="left">3</td>
<td align="center">2013-05-17</td>
<td align="center">Q7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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">
<td align="left">6</td>
<td align="center">2013-08-07</td>
<td align="center">R7</td>
<td align="center">Hospital A</td>
<td align="left">4</td>
<td align="center">2013-01-27</td>
<td align="center">T4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
@@ -737,16 +737,16 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2017-01-17</td>
<td align="center">S7</td>
<td align="center">Hospital C</td>
<td align="left">9</td>
<td align="center">2011-04-24</td>
<td align="center">K8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@@ -754,9 +754,9 @@ like:</p>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2012-04-17</td>
<td align="center">C5</td>
<td align="center">Hospital A</td>
<td align="center">2014-08-22</td>
<td align="center">M5</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
@@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,584<br>
Available: 10,584 (100%, NA: 0 = 0%)<br>
Length: 10,610<br>
Available: 10,610 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,624</td>
<td align="right">43.69%</td>
<td align="right">4,624</td>
<td align="right">43.69%</td>
<td align="right">4,654</td>
<td align="right">43.86%</td>
<td align="right">4,654</td>
<td align="right">43.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,728</td>
<td align="right">25.77%</td>
<td align="right">7,352</td>
<td align="right">69.46%</td>
<td align="right">2,681</td>
<td align="right">25.27%</td>
<td align="right">7,335</td>
<td align="right">69.13%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,086</td>
<td align="right">19.71%</td>
<td align="right">9,438</td>
<td align="right">89.17%</td>
<td align="right">2,113</td>
<td align="right">19.92%</td>
<td align="right">9,448</td>
<td align="right">89.05%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,146</td>
<td align="right">10.83%</td>
<td align="right">10,584</td>
<td align="right">1,162</td>
<td align="right">10.95%</td>
<td align="right">10,610</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@@ -874,14 +874,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="10%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@@ -902,38 +902,23 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-01-17</td>
<td align="center">S7</td>
<td align="center">Hospital C</td>
<td align="center">2011-04-24</td>
<td align="center">K8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-01-20</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-10-21</td>
<td align="center">V1</td>
<td align="center">2012-10-31</td>
<td align="center">S10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
@@ -946,10 +931,40 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-11-07</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-12-07</td>
<td align="center">Z2</td>
<td align="center">Hospital B</td>
<td align="center">2014-02-28</td>
<td align="center">Q8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-04-14</td>
<td align="center">O4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@@ -961,31 +976,16 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-01-12</td>
<td align="center">D9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-11-16</td>
<td align="center">T8</td>
<td align="center">Hospital C</td>
<td align="center">2012-07-02</td>
<td align="center">I5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2203</td>
<td align="center">122</td>
<td align="center">2299</td>
<td align="center">4624</td>
<td align="center">2202</td>
<td align="center">129</td>
<td align="center">2323</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3430</td>
<td align="center">149</td>
<td align="center">1045</td>
<td align="center">4624</td>
<td align="center">3443</td>
<td align="center">153</td>
<td align="center">1058</td>
<td align="center">4654</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3361</td>
<td align="center">3360</td>
<td align="center">0</td>
<td align="center">1263</td>
<td align="center">4624</td>
<td align="center">1294</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4052</td>
<td align="center">4089</td>
<td align="center">0</td>
<td align="center">572</td>
<td align="center">4624</td>
<td align="center">565</td>
<td align="center">4654</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1146</td>
<td align="center">1146</td>
<td align="center">1162</td>
<td align="center">1162</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">901</td>
<td align="center">30</td>
<td align="center">215</td>
<td align="center">1146</td>
<td align="center">928</td>
<td align="center">43</td>
<td align="center">191</td>
<td align="center">1162</td>
</tr>
</tbody>
</table>
@@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4052</td>
<td align="center">4089</td>
<td align="center">0</td>
<td align="center">572</td>
<td align="center">4624</td>
<td align="center">565</td>
<td align="center">4654</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1033</td>
<td align="center">1041</td>
<td align="center">0</td>
<td align="center">113</td>
<td align="center">1146</td>
<td align="center">121</td>
<td align="center">1162</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2440</td>
<td align="center">2383</td>
<td align="center">0</td>
<td align="center">288</td>
<td align="center">2728</td>
<td align="center">298</td>
<td align="center">2681</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2086</td>
<td align="center">2086</td>
<td align="center">2113</td>
<td align="center">2113</td>
</tr>
</tbody>
</table>
@@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5409108</span></span></code></pre></div>
<span><span class="co"># [1] 0.5454288</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5492958</td>
<td align="center">0.5398258</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5316054</td>
<td align="center">0.5561224</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5598456</td>
<td align="center">0.5287860</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5306719</td>
<td align="center">0.5477338</td>
</tr>
</tbody>
</table>
@@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5492958</td>
<td align="center">3195</td>
<td align="center">0.5398258</td>
<td align="center">3214</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5316054</td>
<td align="center">3781</td>
<td align="center">0.5561224</td>
<td align="center">3724</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5598456</td>
<td align="center">1554</td>
<td align="center">0.5287860</td>
<td align="center">1598</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5306719</td>
<td align="center">2054</td>
<td align="center">0.5477338</td>
<td align="center">2074</td>
</tr>
</tbody>
</table>
@@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7740052</td>
<td align="center">0.8762976</td>
<td align="center">0.9744810</td>
<td align="center">0.7726687</td>
<td align="center">0.8785991</td>
<td align="center">0.9804469</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8123909</td>
<td align="center">0.9013962</td>
<td align="center">0.9816754</td>
<td align="center">0.8356282</td>
<td align="center">0.8958692</td>
<td align="center">0.9870912</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7840909</td>
<td align="center">0.8944282</td>
<td align="center">0.9783724</td>
<td align="center">0.7967176</td>
<td align="center">0.8888474</td>
<td align="center">0.9813502</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5421860</td>
<td align="center">0.5224799</td>
<td align="center">0.0000000</td>
<td align="center">0.5421860</td>
<td align="center">0.5224799</td>
</tr>
</tbody>
</table>
@@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.9%</td>
<td align="right">27.1%</td>
<td align="right">54.0%</td>
<td align="right">26.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">53.2%</td>
<td align="right">26.0%</td>
<td align="right">55.6%</td>
<td align="right">26.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.0%</td>
<td align="right">27.3%</td>
<td align="right">52.9%</td>
<td align="right">23.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.1%</td>
<td align="right">25.7%</td>
<td align="right">54.8%</td>
<td align="right">27.0%</td>
</tr>
</tbody>
</table>
@@ -1410,16 +1410,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class 'mic'</span></span>
<span><span class="co"># [1] 64 0.001 4 64 0.01 0.01 0.0625 0.5 0.001 0.005 </span></span>
<span><span class="co"># [11] 0.5 1 64 8 0.01 1 0.001 0.002 0.5 256 </span></span>
<span><span class="co"># [21] 0.5 0.025 0.025 128 0.001 4 256 0.005 64 0.125 </span></span>
<span><span class="co"># [31] 128 0.005 0.005 8 0.025 2 0.001 256 0.002 256 </span></span>
<span><span class="co"># [41] 0.025 0.125 128 128 0.0625 0.25 0.0625 0.025 128 0.5 </span></span>
<span><span class="co"># [51] 2 0.005 0.0625 0.0625 0.002 1 1 1 256 64 </span></span>
<span><span class="co"># [61] 8 0.001 1 32 0.001 0.125 0.25 32 0.005 32 </span></span>
<span><span class="co"># [71] 0.002 128 0.25 16 0.01 0.01 0.0625 64 0.01 16 </span></span>
<span><span class="co"># [81] 128 0.005 0.002 4 0.25 0.125 0.001 0.5 0.005 0.125 </span></span>
<span><span class="co"># [91] 0.001 0.001 0.01 0.001 0.5 0.125 0.005 256 128 8</span></span></code></pre></div>
<span><span class="co"># [1] 0.002 0.002 0.25 0.01 0.5 &lt;=0.001 0.25 &gt;=256 0.0625 </span></span>
<span><span class="co"># [10] 0.25 0.25 16 8 0.002 8 0.5 0.125 0.005 </span></span>
<span><span class="co"># [19] 16 0.01 16 64 0.125 0.005 0.5 16 0.5 </span></span>
<span><span class="co"># [28] 0.01 &gt;=256 0.0625 32 0.005 0.25 128 0.002 2 </span></span>
<span><span class="co"># [37] 1 8 128 &gt;=256 0.025 0.025 32 1 0.005 </span></span>
<span><span class="co"># [46] 0.0625 32 &gt;=256 0.01 4 0.01 16 &lt;=0.001 0.002 </span></span>
<span><span class="co"># [55] 0.002 &gt;=256 2 32 2 0.125 64 &lt;=0.001 0.5 </span></span>
<span><span class="co"># [64] 16 0.01 0.25 4 0.002 0.5 8 2 64 </span></span>
<span><span class="co"># [73] 0.01 0.125 &lt;=0.001 16 0.005 32 0.01 4 1 </span></span>
<span><span class="co"># [82] 1 0.025 128 0.125 8 64 0.125 2 0.125 </span></span>
<span><span class="co"># [91] 2 4 0.0625 &lt;=0.001 &gt;=256 0.25 0.5 0.025 &lt;=0.001</span></span>
<span><span class="co"># [100] 4</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@@ -1453,10 +1455,10 @@ plotting:</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class 'disk'</span></span>
<span><span class="co"># [1] 20 17 20 22 27 22 22 26 23 30 22 28 20 31 29 21 21 26 23 18 23 23 26 18 17</span></span>
<span><span class="co"># [26] 22 24 27 25 25 31 24 22 29 22 19 24 31 17 27 26 23 21 28 26 22 26 19 25 22</span></span>
<span><span class="co"># [51] 25 29 17 30 30 21 29 23 24 29 29 31 17 19 21 21 23 21 31 18 25 23 31 27 31</span></span>
<span><span class="co"># [76] 19 28 20 29 26 30 29 18 29 31 21 25 27 27 23 22 28 21 24 19 31 20 19 20 26</span></span></code></pre></div>
<span><span class="co"># [1] 23 30 18 26 21 18 21 17 30 30 30 22 23 17 26 18 30 27 26 31 26 30 23 22 17</span></span>
<span><span class="co"># [26] 27 27 26 30 17 18 19 26 29 29 24 20 30 27 22 18 31 26 24 26 22 30 23 20 22</span></span>
<span><span class="co"># [51] 17 22 17 31 18 19 31 17 24 17 31 28 28 20 23 18 25 21 31 30 21 25 25 30 20</span></span>
<span><span class="co"># [76] 22 30 27 24 26 29 19 23 20 31 24 19 22 27 29 28 18 29 26 22 19 20 24 19 27</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
articles/AMR_files/figure-html/disk_plots-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 38 KiB

After

Width:  |  Height:  |  Size: 38 KiB

articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 54 KiB

After

Width:  |  Height:  |  Size: 55 KiB

articles/AMR_files/figure-html/mic_plots-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 27 KiB

After

Width:  |  Height:  |  Size: 27 KiB

articles/AMR_files/figure-html/mic_plots-2.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 36 KiB

After

Width:  |  Height:  |  Size: 37 KiB

articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 37 KiB

After

Width:  |  Height:  |  Size: 37 KiB

articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 48 KiB

After

Width:  |  Height:  |  Size: 50 KiB

articles/AMR_files/figure-html/plot 1-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 42 KiB

After

Width:  |  Height:  |  Size: 42 KiB

articles/AMR_files/figure-html/plot 3-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 28 KiB

After

Width:  |  Height:  |  Size: 28 KiB

articles/AMR_files/figure-html/plot 4-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 76 KiB

After

Width:  |  Height:  |  Size: 76 KiB

articles/AMR_files/figure-html/plot 5-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 49 KiB

After

Width:  |  Height:  |  Size: 49 KiB

articles/EUCAST.html
+1 -1
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/MDR.html
+27 -27
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 R R R I I R</span></span>
<span><span class="co"># 2 I R R S I S</span></span>
<span><span class="co"># 3 S I I R I S</span></span>
<span><span class="co"># 4 I S R I I R</span></span>
<span><span class="co"># 5 I R R R R S</span></span>
<span><span class="co"># 6 R S R R S I</span></span>
<span><span class="co"># 1 S S R R R S</span></span>
<span><span class="co"># 2 R R I I R R</span></span>
<span><span class="co"># 3 S S R I R I</span></span>
<span><span class="co"># 4 S I R I R R</span></span>
<span><span class="co"># 5 R S R R I I</span></span>
<span><span class="co"># 6 S S S R I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -436,32 +436,32 @@ Unique: 5</p>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1000</td>
<td align="right">20.00%</td>
<td align="right">4228</td>
<td align="right">84.56%</td>
<td align="right">968</td>
<td align="right">19.36%</td>
<td align="right">4196</td>
<td align="right">83.92%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">458</td>
<td align="right">9.16%</td>
<td align="right">4686</td>
<td align="right">93.72%</td>
<td align="right">452</td>
<td align="right">9.04%</td>
<td align="right">4648</td>
<td align="right">92.96%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">216</td>
<td align="right">4.32%</td>
<td align="right">4902</td>
<td align="right">98.04%</td>
<td align="right">244</td>
<td align="right">4.88%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">98</td>
<td align="right">1.96%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
articles/PCA.html
+1 -1
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/SPSS.html
+1 -1
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/WHONET.html
+1 -1
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/datasets.html
+1 -1
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/index.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/resistance_predict.html
+1 -1
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
articles/welcome_to_AMR.html
+1 -1
View File
@@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
authors.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
index.html
+1 -1
View File
@@ -42,7 +42,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
news/index.html
+6 -6
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -132,10 +132,10 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="1.8.2.9058" id="amr-1829058">AMR 1.8.2.9058<a class="anchor" aria-label="anchor" href="#amr-1829058"></a></h2>
<h2 class="pkg-version" data-toc-text="1.8.2.9059" id="amr-1829059">AMR 1.8.2.9059<a class="anchor" aria-label="anchor" href="#amr-1829059"></a></h2>
<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
<div class="section level4">
<h4 id="breaking-1-8-2-9058">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9058"></a></h4>
<h4 id="breaking-1-8-2-9059">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9059"></a></h4>
<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
@@ -151,7 +151,7 @@
<li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-8-2-9058">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9058"></a></h4>
<h4 id="new-1-8-2-9059">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9059"></a></h4>
<ul><li>
<strong>EUCAST 2022 and CLSI 2022 guidelines</strong> have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules.</li>
<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.</li>
@@ -193,7 +193,7 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="changes-1-8-2-9058">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9058"></a></h4>
<h4 id="changes-1-8-2-9059">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9059"></a></h4>
<ul><li>For <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:
<ul><li>Fixed certain EUCAST breakpoints for MIC values</li>
<li>Allow <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
@@ -232,7 +232,7 @@
<li>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-2-9058">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9058"></a></h4>
<h4 id="other-1-8-2-9059">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9059"></a></h4>
<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
<li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
pkgdown.yml
+1 -1
View File
@@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2022-12-09T12:41Z
last_built: 2022-12-09T14:14Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
reference/AMR-deprecated.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/AMR.html
+1 -1
View File
@@ -62,7 +62,7 @@ Principal component analysis for AMR
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/Rplot005.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 13 KiB

After

Width:  |  Height:  |  Size: 13 KiB

reference/Rplot006.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 12 KiB

After

Width:  |  Height:  |  Size: 12 KiB

reference/Rplot007.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 14 KiB

After

Width:  |  Height:  |  Size: 13 KiB

reference/Rplot008.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 19 KiB

After

Width:  |  Height:  |  Size: 18 KiB

reference/Rplot009.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 8.5 KiB

After

Width:  |  Height:  |  Size: 7.9 KiB

reference/WHOCC.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/WHONET.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/ab_from_text.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/ab_property.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/add_custom_antimicrobials.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/age.html
+11 -11
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -195,16 +195,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1996-03-04 26 26.76712 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1942-04-19 80 80.64110 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1931-08-02 91 91.35342 68</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1976-12-11 45 45.99452 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1978-12-19 43 43.97260 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1958-05-13 64 64.57534 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1951-12-07 71 71.00548 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1962-12-05 60 60.01096 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1951-09-05 71 71.26027 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1967-10-18 55 55.14247 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1976-08-21 46 46.30137 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-03-07 69 69.75890 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1940-02-25 82 82.78630 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1972-05-17 50 50.56438 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1944-12-05 78 78.01096 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1991-05-13 31 31.57534 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1960-07-24 62 62.37808 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1982-06-27 40 40.45205 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1993-07-18 29 29.39452 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1951-10-24 71 71.12603 48</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/age_groups.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/antibiotic_class_selectors.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/antibiotics.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.ab.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.av.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.disk.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.mic.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.mo.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.rsi.html
+11 -11
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-09 <span style="color: #949494;">12:41:48</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-09 <span style="color: #949494;">12:41:49</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-09 <span style="color: #949494;">12:41:49</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-09 <span style="color: #949494;">12:41:50</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-09 <span style="color: #949494;">12:41:50</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-09 <span style="color: #949494;">12:41:50</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-09 <span style="color: #949494;">12:41:51</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-09 <span style="color: #949494;">12:41:51</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-09 <span style="color: #949494;">12:41:51</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-09 <span style="color: #949494;">12:41:51</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-09 <span style="color: #949494;">14:14:44</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-09 <span style="color: #949494;">14:14:46</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-09 <span style="color: #949494;">14:14:46</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-09 <span style="color: #949494;">14:14:46</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-09 <span style="color: #949494;">14:14:46</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-09 <span style="color: #949494;">14:14:46</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span>
reference/atc_online.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/av_from_text.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/av_property.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/availability.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/bug_drug_combinations.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/count.html
+1 -1
View File
@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/custom_eucast_rules.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/dosage.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/eucast_rules.html
+1 -1
View File
@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/example_isolates.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/example_isolates_unclean.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/first_isolate.html
+1 -1
View File
@@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/g.test.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/get_episode.html
+72 -72
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -182,42 +182,42 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 23 4 57 10 24 33 54 46 15 13 52 3 46 30 17 43 31 50 27 6 44 18 9 40 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 5 32 49 49 9 23 27 8 8 22 53 26 58 1 59 49 59 5 35 22 11 43 60 54 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 51 26 18 43 2 22 47 28 36 22 15 1 40 23 41 34 60 32 45 9 51 21 50 24 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 42 26 29 58 31 13 59 4 55 38 10 19 54 29 7 53 50 55 15 40 4 46 55 61 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 14 43 54 45 54 10 23 55 18 48 9 33 29 7 6 41 39 28 59 7 62 6 41 57 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 60 41 35 37 15 45 49 24 36 10 25 22 20 52 14 62 8 6 42 60 12 41 14 32 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 59 58 9 13 13 21 36 3 49 12 1 9 57 3 17 23 14 13 62 56 57 40 6 13 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 19 57 24 47 59 20 61 46 54 58 48 30 39 4 32 42 25 4 22 20 56 3 16 44 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 63 45 25 27 5 60 43 43 48 65 20 11 34 1 35 24 32 57 55 12 31 41 31 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 5 3 19 45 49 66 55 20 49 1 4 3 16 37 35 25 61 63 1 37 36 20 22 3 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 64 11 12 40 61 16 15 21 26 57 2 44 1 49 35 21 29 7 17 15 13 48 10 20 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 29 45 14 40 59 65 26 52 49 7 33 29 14 9 17 46 51 18 65 3 38 6 12 11 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 52 5 64 57 22 26 58 7 21 30 16 8 54 33 19 11 41 10 59 34 64 38 64 57 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 51 14 18 54 9 6 23 53 44 21 36 63 48 62 19 7 36 7 11 49 58 34 34 37 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 31 45 22 24 4 58 54 22 22 56 14 14 62 32 23 63 1 8 61 41 28 11 30 26 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 39 14 42 49 25 49 52 43 18 11 38 55 11 56 59 54 15 9 48 60 50 4 7 18 57</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-08-31 149442 80 F ICU B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-09-24 CF9318 29 M ICU B_CMPYL_JEJN NA NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-10-11 871360 78 M Clinical B_STPHY_EPDR R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-08-28 390178 57 M Clinical B_STRPT_SLVR S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-05-16 E52286 47 M Clinical B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-05-22 F35553 50 M ICU B_STPHY_EPDR R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-05-16 D25302 65 F ICU B_STRPT_ANGN S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-06-07 710157 76 M Outpatie… B_STPHY_CONS S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -253,16 +253,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 403631 2007-07-31 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 304347 2002-11-04 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 964129 2016-06-21 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 189363 2004-03-17 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 80C025 2007-11-13 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 284FFF 2010-03-31 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> A76045 2015-10-06 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 959835 2013-11-16 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 277241 2005-09-01 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 696587 2004-11-16 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 399817 2004-04-15 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C95287 2017-03-14 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A95779 2012-05-18 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 636118 2007-06-17 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 921720 2007-11-02 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 600057 2002-11-28 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D10538 2016-08-13 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 146120 2011-09-23 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 685406 2011-09-27 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C01360 2013-07-27 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -274,19 +274,19 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [179]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-07-31 403631 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-11-04 304347 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2016-06-21 964129 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2004-03-17 189363 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-11-13 80C025 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-03-31 284FFF 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2015-10-06 A76045 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2013-11-16 959835 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2005-09-01 277241 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2004-11-16 696587 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [185]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2004-04-15 399817 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2017-03-14 C95287 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2012-05-18 A95779 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2007-06-17 636118 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-11-02 921720 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2002-11-28 600057 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2016-08-13 D10538 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2011-09-23 146120 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2011-09-27 685406 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2013-07-27 C01360 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -301,9 +301,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 112 14 57 81</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 53 13 37 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 14 8 11 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 104 14 53 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 65 12 40 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 16 9 16 16</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@@ -322,7 +322,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
@@ -333,19 +333,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [186]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 403631 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 304347 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 964129 B_SERRT_MRCS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 189363 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 80C025 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 284FFF B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> A76045 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 959835 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 277241 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 696587 B_ESCHR_COLI ICU FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [193]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 399817 B_CTRBC_FRND Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C95287 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A95779 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 636118 B_MRGNL_MRGN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 921720 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 600057 B_STPHY_AURS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D10538 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 146120 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 685406 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C01360 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
reference/ggplot_pca.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/ggplot_rsi.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/guess_ab_col.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/index.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/intrinsic_resistant.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/italicise_taxonomy.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/join.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/key_antimicrobials.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/kurtosis.html
+3 -3
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -172,9 +172,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.991918</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.143253</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0630367</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.07895301</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/like.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mdro.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mean_amr_distance.html
+39 -40
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -200,11 +200,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=128 2 32 &lt;=0.002 64 &lt;=0.002 0.005 8 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 &gt;=2 0.005 0.01 &gt;=2 1 0.5 0.001 0.001 0.002</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.0898120 0.1928148 0.7908130 -1.2970653 0.9403125 -1.2970653</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.0994377 0.4918139 -0.7523105 0.9403125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.3309983 1.2029031 -0.6812519 -0.4632756 1.2029031 0.9849269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.7669507 -1.1873769 -1.1873769 -0.9694007</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -214,38 +213,38 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &lt;=0.0625 0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.5 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 &lt;=0.0625 0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 0.25 0.25 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 0.5 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.0625 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=32 0.5 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 1 0.5 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.25 0.25 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 32 0.25 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 &gt;=1 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 2 &gt;=1 &lt;=0.5 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.5 1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=64 &gt;=1 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 1 0.25 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.5 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 32 &lt;=0.125 1 2</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.15596821 -0.35223027 -0.06296188 -0.77906287 -0.19333099 1.00776983</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.64235988 0.64363737 1.00124386 -0.46673697</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12196526 0.40284317 -0.47762168 -0.30700434 -0.06650357 0.79277984</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.73763891 0.32070406 0.19485787 -0.24438169</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 &lt;=0.0625 0.5 &lt;=0.5 -0.77906287</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.0625 0.5 1 -0.64235988</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.25 0.25 4 -0.46673697</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.5 0.5 1 -0.35223027</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 0.25 0.25 &gt;=16 -0.19333099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &lt;=0.0625 0.5 4 -0.15596821</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 0.5 &lt;=0.5 -0.06296188</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=32 0.5 1 2 0.64363737</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 1 0.5 &gt;=16 1.00124386</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 0.5 4 4 1.00776983</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 1 0.25 2 &lt;=1 -0.73763891</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 2 &gt;=1 &lt;=0.5 &lt;=1 -0.47762168</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.5 1 &lt;=1 -0.30700434</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 32 &lt;=0.125 1 2 -0.24438169</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 1 &lt;=1 -0.06650357</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 32 0.25 &lt;=0.5 4 0.12196526</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.5 &gt;=8 &lt;=1 0.19485787</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2 0.32070406</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 &gt;=1 1 4 0.40284317</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=64 &gt;=1 &gt;=8 &lt;=1 0.79277984</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -257,17 +256,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 16 0.5 0.5 &lt;=0.5 -0.06296188 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A 16 &lt;=0.0625 0.5 4 -0.15596821 0.09300632</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 E 4 0.25 0.25 &gt;=16 -0.19333099 0.13036910</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B 4 0.5 0.5 1 -0.35223027 0.28926839</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J 4 0.25 0.25 4 -0.46673697 0.40377508</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G 8 &lt;=0.0625 0.5 1 -0.64235988 0.57939799</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 H &gt;=32 0.5 1 2 0.64363737 0.70659925</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 8 &lt;=0.0625 0.5 &lt;=0.5 -0.77906287 0.71610098</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 1 0.5 &gt;=16 1.00124386 1.06420574</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F 16 0.5 4 4 1.00776983 1.07073172</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 2 &gt;=1 &lt;=0.5 &lt;=1 -0.47762168 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D 8 0.5 1 &lt;=1 -0.30700434 0.1706173</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 32 &lt;=0.125 1 2 -0.24438169 0.2332400</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 1 0.25 2 &lt;=1 -0.73763891 0.2600172</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 1 &lt;=1 -0.06650357 0.4111181</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A 32 0.25 &lt;=0.5 4 0.12196526 0.5995869</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 I 8 0.5 &gt;=8 &lt;=1 0.19485787 0.6724795</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2 0.32070406 0.7983257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B 4 &gt;=1 1 4 0.40284317 0.8804648</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F &gt;=64 &gt;=1 &gt;=8 &lt;=1 0.79277984 1.2704015</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
reference/microorganisms.codes.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/microorganisms.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mo_matching_score.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mo_property.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mo_source.html
+1 -1
View File
@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/pca.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/plot-1.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 26 KiB

After

Width:  |  Height:  |  Size: 27 KiB

reference/plot-2.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 26 KiB

After

Width:  |  Height:  |  Size: 26 KiB

reference/plot-3.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 27 KiB

After

Width:  |  Height:  |  Size: 28 KiB

reference/plot-4.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 37 KiB

After

Width:  |  Height:  |  Size: 38 KiB

reference/plot-5.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 37 KiB

After

Width:  |  Height:  |  Size: 37 KiB

reference/plot-6.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 36 KiB

After

Width:  |  Height:  |  Size: 36 KiB

reference/plot-7.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 38 KiB

After

Width:  |  Height:  |  Size: 37 KiB

reference/plot-8.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 56 KiB

After

Width:  |  Height:  |  Size: 54 KiB

reference/plot-9.png
BIN
View File
Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 26 KiB

After

Width:  |  Height:  |  Size: 24 KiB

reference/plot.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/proportion.html
+1 -1
View File
@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/random.html
+19 -17
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -183,42 +183,44 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.25 0.01 8 128 0.025 0.5 &lt;=0.002 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 16 0.005 0.005 0.025 0.025 0.25 0.025 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 256 256 2 256 0.005 0.025 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 64 0.0625 0.025 0.25 0.025 0.01 0.005 128 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 64 32 0.125 0.002 0.005 64 0.0625 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.125 128 0.0625 &lt;=0.001 0.002 0.0625 0.25 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 16 47 35 37 49 26 34 44 48 27 44 26 41 49 23 7 50 19 34 38 25 21 43 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 47 11 44 36 21 24 31 13 40 21 42 33 36 18 41 40 15 19 26 48 8 11 37 46</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R S S S S I S S R R R I S S S S S S S S R I R I S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I S R R I S R I R I R R R I R I R S R R R I S S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 128 0.001 0.01 128 0.01 0.001 0.01 4 128 0.001 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.002 4 16 32 1 0.25 1 2 64 16 64 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 0.5 0.01 16 8 0.0625 &lt;=0.001 0.0625 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 4 8 &lt;=0.001 0.002 4 &lt;=0.001 0.0625 8 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.01 0.01 &lt;=0.001 0.002 0.025 2 0.5 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=1 8 8 8 &lt;=1 2 4 8 &gt;=16 &gt;=16 2 4 8 &gt;=16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 4 2 &gt;=16 4 &lt;=1 2 &gt;=16 8 8 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 16 16 8 16 1 8 8 4 16 4 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 1 &lt;=0.5 4 &lt;=0.5 16 1 2 8 16 &lt;=0.5 2 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 &gt;=16 &gt;=16 4 2 0.5 0.5 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 0.5 &lt;=0.125 2 4 &gt;=16 4 8 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 1 &lt;=0.125 0.5 0.5 0.5 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 4 0.25 &lt;=0.0625 16 &lt;=0.0625 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 0.5 0.125 8 1 0.25 0.5 8 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] &lt;=0.0625 0.125 0.25 0.25 0.5 16 0.125 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &lt;=0.0625</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21 36 49 10 16 15 34 46 43 42 33 47 43 50 19 45 45 13 34 9 46 20 42 40 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 26 37 31 35 32 48 43 11 17 25 20 47 27 30 44 48 41 47 46 45 37 41 13 28</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 11 16 13 11 12 11 14 13 11 14 11 12 15 12 12 13 13 17 17 16 13 16 11 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 16 14 12 17 11 14 11 12 11 16 12 16 11 16 12 14 17 12 13 14 15 17 15 11</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 15 25 23 16 23 16 27 26 20 17 16 22 22 27 18 24 17 26 25 27 21 16 27 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 22 20 23 18 16 19 27 17 16 24 16 27 16 17 17 15 19 15 15 20 22 24 21 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
reference/resistance_predict.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/rsi_translation.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/skewness.html
+2 -2
View File
@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -171,7 +171,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01115228</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -9.41422e-05</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
reference/translate.html
+1 -1
View File
@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
search.json
+1 -1
View File
@@ -1 +1 @@
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated