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articles/AMR.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="">2.0.0.9044</small>
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@ -38,7 +38,7 @@
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articles/MDR.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="">2.0.0.9044</small>
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@ -402,19 +402,19 @@ 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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 S S I I S S</span></span>
<span><span class="co">#&gt; 2 S I R R I I</span></span>
<span><span class="co">#&gt; 3 I S R I I I</span></span>
<span><span class="co">#&gt; 4 I I R S R S</span></span>
<span><span class="co">#&gt; 5 I S S S R I</span></span>
<span><span class="co">#&gt; 6 I R S S S R</span></span>
<span><span class="co">#&gt; 1 R S I S S S</span></span>
<span><span class="co">#&gt; 2 S S I R I R</span></span>
<span><span class="co">#&gt; 3 I R I I R S</span></span>
<span><span class="co">#&gt; 4 I I I R I S</span></span>
<span><span class="co">#&gt; 5 S R I R R R</span></span>
<span><span class="co">#&gt; 6 S R S I I I</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 6 S</span></span></code></pre></div>
<span><span class="co">#&gt; 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">
@ -455,40 +455,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3236</td>
<td align="right">64.72%</td>
<td align="right">3236</td>
<td align="right">64.72%</td>
<td align="right">3247</td>
<td align="right">64.94%</td>
<td align="right">3247</td>
<td align="right">64.94%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">962</td>
<td align="right">19.24%</td>
<td align="right">4198</td>
<td align="right">83.96%</td>
<td align="right">986</td>
<td align="right">19.72%</td>
<td align="right">4233</td>
<td align="right">84.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">470</td>
<td align="right">9.40%</td>
<td align="right">4668</td>
<td align="right">93.36%</td>
<td align="right">434</td>
<td align="right">8.68%</td>
<td align="right">4667</td>
<td align="right">93.34%</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">4884</td>
<td align="right">97.68%</td>
<td align="right">231</td>
<td align="right">4.62%</td>
<td align="right">4898</td>
<td align="right">97.96%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">116</td>
<td align="right">2.32%</td>
<td align="right">102</td>
<td align="right">2.04%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
articles/PCA.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="">2.0.0.9044</small>
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@ -38,7 +38,7 @@
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articles/datasets.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="">2.0.0.9044</small>
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@ -214,7 +214,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52 169 rows and 23 columns, containing the following
<p>A data set with 52 171 rows and 23 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -224,8 +224,8 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 8 July 2023 15:30:05 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 14 July 2023 08:49:06 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original
@ -302,7 +302,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36 499</td>
<td align="center">36 501</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
@ -2066,27 +2066,27 @@ reality and can be used to practise AMR data analysis.</p>
<code>microorganisms.groups</code>: Species Groups and
Microbiological Complexes<a class="anchor" aria-label="anchor" href="#microorganisms-groups-species-groups-and-microbiological-complexes"></a>
</h2>
<p>A data set with 507 rows and 4 columns, containing the following
<p>A data set with 521 rows and 4 columns, containing the following
column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
<em>mo_name</em>.</p>
<p>This data set is in R available as
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
package.</p>
<p>It was last updated on 12 July 2023 14:04:48 UTC. Find more info
<p>It was last updated on 14 July 2023 08:49:06 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.rds" class="external-link">original
R Data Structure (RDS) file</a> (5 kB)<br>
R Data Structure (RDS) file</a> (6 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.txt" class="external-link">tab-separated
text file</a> (48 kB)<br>
text file</a> (49 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xlsx" class="external-link">Microsoft
Excel workbook</a> (20 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.feather" class="external-link">Apache
Feather file</a> (18 kB)<br>
Feather file</a> (19 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.parquet" class="external-link">Apache
Parquet file</a> (13 kB)<br>
@ -2095,10 +2095,10 @@ Parquet file</a> (13 kB)<br>
transport (XPT) file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.sav" class="external-link">IBM
SPSS Statistics data file</a> (62 kB)<br>
SPSS Statistics data file</a> (64 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.dta" class="external-link">Stata
DTA file</a> (79 kB)</li>
DTA file</a> (81 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>

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articles/index.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -38,7 +38,7 @@
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articles/resistance_predict.html
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@ -38,7 +38,7 @@
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articles/welcome_to_AMR.html
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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