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@ -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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>
@ -381,12 +386,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="28%">
<col width="26%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -401,9 +406,9 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-03-25</td>
<td align="center">M2</td>
<td align="center">Hospital A</td>
<td align="center">2010-08-18</td>
<td align="center">D8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
@ -412,58 +417,58 @@ data set:</p>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-03-28</td>
<td align="center">F10</td>
<td align="center">Hospital A</td>
<td align="center">2011-03-28</td>
<td align="center">H7</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-31</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2016-12-20</td>
<td align="center">M9</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-08-03</td>
<td align="center">V7</td>
<td align="center">2012-11-13</td>
<td align="center">Y5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-06-06</td>
<td align="center">Q7</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-11-23</td>
<td align="center">Z5</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-01-13</td>
<td align="center">X7</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2017-05-04</td>
<td align="center">U8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
</tbody>
@ -500,16 +505,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,396</td>
<td align="right">51.98%</td>
<td align="right">10,396</td>
<td align="right">51.98%</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,604</td>
<td align="right">48.02%</td>
<td align="right">9,625</td>
<td align="right">48.13%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -622,9 +627,9 @@ 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 12,236 'phenotype-based' first isolates (61.2% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,316 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.2% is suitable for resistance analysis! We can now filter
<p>So only 61.6% 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">
@ -635,7 +640,7 @@ 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 12,236 isolates for analysis. Now our data looks
<p>So we end up with 12,316 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>
@ -675,14 +680,14 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2013-03-28</td>
<td align="center">F10</td>
<td align="center">Hospital A</td>
<td align="center">2011-03-28</td>
<td align="center">H7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -690,31 +695,31 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2010-05-31</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="left">6</td>
<td align="center">2017-05-04</td>
<td align="center">U8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2014-08-03</td>
<td align="center">V7</td>
<td align="center">Hospital C</td>
<td align="left">7</td>
<td align="center">2015-09-03</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -722,53 +727,53 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2014-11-23</td>
<td align="center">Z5</td>
<td align="left">8</td>
<td align="center">2010-01-29</td>
<td align="center">D7</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2010-07-28</td>
<td align="center">Q2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</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">8</td>
<td align="center">2012-06-28</td>
<td align="center">Z1</td>
<td align="center">Hospital B</td>
<td align="left">9</td>
<td align="center">2016-12-13</td>
<td align="center">D1</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-01-28</td>
<td align="center">E1</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">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -802,8 +807,8 @@ 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: 12,236<br>
Available: 12,236 (100%, NA: 0 = 0%)<br>
Length: 12,316<br>
Available: 12,316 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -828,33 +833,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,810</td>
<td align="right">47.48%</td>
<td align="right">5,810</td>
<td align="right">47.48%</td>
<td align="right">5,959</td>
<td align="right">48.38%</td>
<td align="right">5,959</td>
<td align="right">48.38%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,302</td>
<td align="right">26.99%</td>
<td align="right">9,112</td>
<td align="right">74.47%</td>
<td align="right">3,259</td>
<td align="right">26.46%</td>
<td align="right">9,218</td>
<td align="right">74.85%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,840</td>
<td align="right">15.04%</td>
<td align="right">10,952</td>
<td align="right">89.51%</td>
<td align="right">1,827</td>
<td align="right">14.83%</td>
<td align="right">11,045</td>
<td align="right">89.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,284</td>
<td align="right">10.49%</td>
<td align="right">12,236</td>
<td align="right">1,271</td>
<td align="right">10.32%</td>
<td align="right">12,316</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -875,14 +880,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -903,13 +908,58 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-05-31</td>
<td align="center">N4</td>
<td align="center">Hospital B</td>
<td align="center">2017-05-04</td>
<td align="center">U8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-09-03</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-01-29</td>
<td align="center">D7</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">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">2012-05-22</td>
<td align="center">G6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -917,76 +967,31 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-11-23</td>
<td align="center">Z5</td>
<tr class="odd">
<td align="center">2010-01-09</td>
<td align="center">L8</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_STPHY_AURS</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2015-03-09</td>
<td align="center">S9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</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">2015-03-21</td>
<td align="center">K1</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">2015-02-07</td>
<td align="center">G7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-10-03</td>
<td align="center">G8</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">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">2012-11-05</td>
<td align="center">F10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -1014,50 +1019,50 @@ 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">1492</td>
<td align="center">1218</td>
<td align="center">3100</td>
<td align="center">5810</td>
<td align="center">1510</td>
<td align="center">1283</td>
<td align="center">3166</td>
<td align="center">5959</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2743</td>
<td align="center">1143</td>
<td align="center">1924</td>
<td align="center">5810</td>
<td align="center">2778</td>
<td align="center">1154</td>
<td align="center">2027</td>
<td align="center">5959</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2024</td>
<td align="center">1859</td>
<td align="center">1927</td>
<td align="center">5810</td>
<td align="center">2112</td>
<td align="center">1820</td>
<td align="center">2027</td>
<td align="center">5959</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2037</td>
<td align="center">1738</td>
<td align="center">2035</td>
<td align="center">5810</td>
<td align="center">2063</td>
<td align="center">1825</td>
<td align="center">2071</td>
<td align="center">5959</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">1284</td>
<td align="center">1284</td>
<td align="center">1271</td>
<td align="center">1271</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">556</td>
<td align="center">263</td>
<td align="center">465</td>
<td align="center">1284</td>
<td align="center">579</td>
<td align="center">266</td>
<td align="center">426</td>
<td align="center">1271</td>
</tr>
</tbody>
</table>
@ -1079,34 +1084,34 @@ 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">2037</td>
<td align="center">1738</td>
<td align="center">2035</td>
<td align="center">5810</td>
<td align="center">2063</td>
<td align="center">1825</td>
<td align="center">2071</td>
<td align="center">5959</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">429</td>
<td align="center">422</td>
<td align="center">433</td>
<td align="center">1284</td>
<td align="center">402</td>
<td align="center">411</td>
<td align="center">458</td>
<td align="center">1271</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1099</td>
<td align="center">1066</td>
<td align="center">1137</td>
<td align="center">3302</td>
<td align="center">1171</td>
<td align="center">1032</td>
<td align="center">1056</td>
<td align="center">3259</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">1840</td>
<td align="center">1840</td>
<td align="center">1827</td>
<td align="center">1827</td>
</tr>
</tbody>
</table>
@ -1138,7 +1143,7 @@ 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] 0.5813992</span></span></code></pre></div>
<span><span class="co"># [1] 0.5802209</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">
@ -1153,19 +1158,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5883615</td>
<td align="center">0.5650667</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5790089</td>
<td align="center">0.5838028</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5716704</td>
<td align="center">0.5864369</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5820106</td>
<td align="center">0.5923414</td>
</tr>
</tbody>
</table>
@ -1190,23 +1195,23 @@ 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">0.5883615</td>
<td align="center">3729</td>
<td align="center">0.5650667</td>
<td align="center">3750</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5790089</td>
<td align="center">4278</td>
<td align="center">0.5838028</td>
<td align="center">4260</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5716704</td>
<td align="center">1772</td>
<td align="center">0.5864369</td>
<td align="center">1799</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5820106</td>
<td align="center">2457</td>
<td align="center">0.5923414</td>
<td align="center">2507</td>
</tr>
</tbody>
</table>
@ -1231,27 +1236,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6688468</td>
<td align="center">0.6497418</td>
<td align="center">0.8898451</td>
<td align="center">0.6598423</td>
<td align="center">0.6524585</td>
<td align="center">0.8848800</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6378505</td>
<td align="center">0.6627726</td>
<td align="center">0.8777259</td>
<td align="center">0.6648308</td>
<td align="center">0.6396538</td>
<td align="center">0.8686074</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6741369</td>
<td align="center">0.6556632</td>
<td align="center">0.8885524</td>
<td align="center">0.6738263</td>
<td align="center">0.6759742</td>
<td align="center">0.8922983</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4766304</td>
<td align="center">0.4564860</td>
<td align="center">0.0000000</td>
<td align="center">0.4766304</td>
<td align="center">0.4564860</td>
</tr>
</tbody>
</table>
@ -1279,23 +1284,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">58.8%</td>
<td align="right">36.3%</td>
<td align="right">56.5%</td>
<td align="right">34.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">57.9%</td>
<td align="right">35.7%</td>
<td align="right">58.4%</td>
<td align="right">37.2%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.2%</td>
<td align="right">36.6%</td>
<td align="right">58.6%</td>
<td align="right">37.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.2%</td>
<td align="right">36.6%</td>
<td align="right">59.2%</td>
<td align="right">37.7%</td>
</tr>
</tbody>
</table>
@ -1411,16 +1416,18 @@ 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] 0.001 0.0625 32 0.0625 32 64 &gt;=256 32 4 0.125 </span></span>
<span><span class="co"># [11] 4 32 128 32 0.125 1 0.0625 &gt;=256 16 64 </span></span>
<span><span class="co"># [21] 0.025 64 16 16 &gt;=256 128 0.025 0.005 0.25 1 </span></span>
<span><span class="co"># [31] 0.5 32 0.0625 16 128 0.025 0.25 1 0.005 0.0625</span></span>
<span><span class="co"># [41] 0.025 0.025 0.25 0.002 0.001 2 8 32 0.0625 0.002 </span></span>
<span><span class="co"># [51] 0.001 0.5 0.25 16 0.125 0.005 64 1 0.0625 0.001 </span></span>
<span><span class="co"># [61] 0.025 32 16 &gt;=256 0.005 0.002 16 &gt;=256 1 0.125 </span></span>
<span><span class="co"># [71] 2 0.125 16 16 64 64 0.0625 0.5 1 0.005 </span></span>
<span><span class="co"># [81] 64 0.125 0.025 0.01 0.0625 0.5 0.002 0.25 0.25 128 </span></span>
<span><span class="co"># [91] 4 16 0.002 0.25 32 32 128 128 0.125 0.25</span></span></code></pre></div>
<span><span class="co"># [1] &lt;=0.001 0.025 128 0.125 0.0625 8 0.025 32 &gt;=256 </span></span>
<span><span class="co"># [10] 4 32 0.005 4 2 32 0.5 0.0625 128 </span></span>
<span><span class="co"># [19] 0.01 16 1 0.01 64 0.0625 8 &gt;=256 0.005 </span></span>
<span><span class="co"># [28] 128 &lt;=0.001 8 1 0.025 1 64 128 0.0625 </span></span>
<span><span class="co"># [37] 2 0.125 4 4 4 16 0.0625 16 0.0625 </span></span>
<span><span class="co"># [46] 0.5 0.5 &lt;=0.001 64 8 128 1 64 2 </span></span>
<span><span class="co"># [55] 1 &gt;=256 &lt;=0.001 0.002 0.5 4 4 32 &lt;=0.001</span></span>
<span><span class="co"># [64] 16 0.002 128 128 4 0.002 8 8 0.0625 </span></span>
<span><span class="co"># [73] 0.002 0.0625 8 16 0.125 0.005 8 &gt;=256 8 </span></span>
<span><span class="co"># [82] 0.01 0.025 0.005 64 1 0.025 0.002 16 32 </span></span>
<span><span class="co"># [91] 0.005 32 0.002 &lt;=0.001 0.25 4 &lt;=0.001 0.25 16 </span></span>
<span><span class="co"># [100] 0.025</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>
@ -1454,10 +1461,10 @@ 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] 18 29 23 17 30 20 29 20 17 19 22 25 29 30 24 22 29 29 24 17 30 19 25 23 26</span></span>
<span><span class="co"># [26] 20 25 17 20 23 27 19 26 19 26 19 21 19 24 20 18 19 30 17 27 29 21 22 29 21</span></span>
<span><span class="co"># [51] 22 30 20 23 27 30 27 19 24 24 21 24 24 17 21 20 31 27 31 20 22 26 25 29 31</span></span>
<span><span class="co"># [76] 31 18 20 18 17 26 25 24 31 20 18 25 26 19 18 23 31 27 18 18 28 30 26 30 27</span></span></code></pre></div>
<span><span class="co"># [1] 29 26 20 20 26 31 29 17 28 21 27 17 30 23 21 19 23 23 20 23 19 27 23 20 23</span></span>
<span><span class="co"># [26] 25 22 25 28 31 19 31 20 31 19 19 28 31 20 29 23 25 28 27 18 24 26 21 30 23</span></span>
<span><span class="co"># [51] 22 31 27 26 27 26 23 22 17 19 18 24 31 25 29 21 29 19 27 20 31 23 23 25 18</span></span>
<span><span class="co"># [76] 31 18 27 31 20 21 23 25 22 31 26 28 21 30 17 31 29 19 25 24 17 19 19 21 21</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>

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29
articles/EUCAST.html
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@ -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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>

87
articles/MDR.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>
@ -375,19 +380,19 @@ 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 I S R I S S</span></span>
<span><span class="co"># 2 I R R I S I</span></span>
<span><span class="co"># 3 I R S I R I</span></span>
<span><span class="co"># 4 S S I S R I</span></span>
<span><span class="co"># 5 I I R I I S</span></span>
<span><span class="co"># 6 R S S S R I</span></span>
<span><span class="co"># 1 I R R R S R</span></span>
<span><span class="co"># 2 R I R S R S</span></span>
<span><span class="co"># 3 R R R I I R</span></span>
<span><span class="co"># 4 I S R R S I</span></span>
<span><span class="co"># 5 S R R S R R</span></span>
<span><span class="co"># 6 S I R I S R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 6 I</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">
@ -428,40 +433,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3130</td>
<td align="right">62.60%</td>
<td align="right">3130</td>
<td align="right">62.60%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1022</td>
<td align="right">20.44%</td>
<td align="right">4152</td>
<td align="right">83.04%</td>
<td align="right">976</td>
<td align="right">19.52%</td>
<td align="right">4203</td>
<td align="right">84.06%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">476</td>
<td align="right">9.52%</td>
<td align="right">4628</td>
<td align="right">92.56%</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4645</td>
<td align="right">92.90%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">269</td>
<td align="right">5.38%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
<td align="right">247</td>
<td align="right">4.94%</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">103</td>
<td align="right">2.06%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

29
articles/PCA.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>

29
articles/SPSS.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>

29
articles/WHONET.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>

29
articles/datasets.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>

29
articles/index.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -32,60 +32,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>

29
articles/resistance_predict.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>

29
articles/welcome_to_AMR.html
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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>