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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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="">2.0.0.9035</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 R R I I R</span></span>
<span><span class="co">#&gt; 2 I R R I S I</span></span>
<span><span class="co">#&gt; 3 I S I R R I</span></span>
<span><span class="co">#&gt; 4 R R I R I S</span></span>
<span><span class="co">#&gt; 5 R S I I I S</span></span>
<span><span class="co">#&gt; 6 I S I S I R</span></span>
<span><span class="co">#&gt; 1 S S I R I I</span></span>
<span><span class="co">#&gt; 2 I I R R S R</span></span>
<span><span class="co">#&gt; 3 I I R R S R</span></span>
<span><span class="co">#&gt; 4 I S I S R S</span></span>
<span><span class="co">#&gt; 5 R R R S S I</span></span>
<span><span class="co">#&gt; 6 I I R S S I</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 4 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 I</span></span></code></pre></div>
<span><span class="co">#&gt; 6 S</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">3187</td>
<td align="right">63.74%</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
<td align="right">3280</td>
<td align="right">65.60%</td>
<td align="right">3280</td>
<td align="right">65.60%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1017</td>
<td align="right">20.34%</td>
<td align="right">4204</td>
<td align="right">84.08%</td>
<td align="right">920</td>
<td align="right">18.40%</td>
<td align="right">4200</td>
<td align="right">84.00%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">456</td>
<td align="right">9.12%</td>
<td align="right">4660</td>
<td align="right">93.20%</td>
<td align="right">459</td>
<td align="right">9.18%</td>
<td align="right">4659</td>
<td align="right">93.18%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">230</td>
<td align="right">4.60%</td>
<td align="right">4890</td>
<td align="right">97.80%</td>
<td align="right">244</td>
<td align="right">4.88%</td>
<td align="right">4903</td>
<td align="right">98.06%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">110</td>
<td align="right">2.20%</td>
<td align="right">97</td>
<td align="right">1.94%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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="">2.0.0.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9038</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">
@ -307,7 +307,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

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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="">2.0.0.9035</small>
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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="">2.0.0.9035</small>
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@ -904,14 +904,14 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 28 885 rows and 12 columns, containing the following
<p>A data set with 29 747 rows and 12 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>method</em>, <em>site</em>,
<em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>,
<em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em>, and
<em>uti</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 12 July 2023 10:41:25 UTC. Find more info
<p>It was last updated on 12 July 2023 14:04:48 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -919,7 +919,7 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (59 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (2.2 MB)<br>
text file</a> (2.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.3 MB)<br>
@ -928,16 +928,16 @@ Excel workbook</a> (1.3 MB)<br>
Feather file</a> (1.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (87 kB)<br>
Parquet file</a> (96 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
transport (XPT) file</a> (7.7 MB)<br>
transport (XPT) file</a> (7.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (4.4 MB)<br>
SPSS Statistics data file</a> (4.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (7.6 MB)</li>
DTA file</a> (7.8 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
@ -959,7 +959,7 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<col width="14%">
<col width="6%">
<col width="2%">
<col width="15%">
<col width="16%">
<col width="8%">
<col width="8%">
<col width="7%">
@ -988,8 +988,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">MEM</td>
<td align="center">Meropenem</td>
@ -1004,8 +1004,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">MEM</td>
<td align="center">Meropenem</td>
@ -1020,8 +1020,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
@ -1036,8 +1036,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
@ -1052,8 +1052,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
@ -1068,8 +1068,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
@ -2046,13 +2046,13 @@ 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 448 rows and 4 columns, containing the following
<p>A data set with 507 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 10:41:25 UTC. Find more info
<p>It was last updated on 12 July 2023 14:04:48 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>
@ -2060,25 +2060,25 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (5 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> (42 kB)<br>
text file</a> (48 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> (18 kB)<br>
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> (17 kB)<br>
Feather file</a> (18 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> (12 kB)<br>
Parquet file</a> (13 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xpt" class="external-link">SAS
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> (54 kB)<br>
SPSS Statistics data file</a> (62 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> (68 kB)</li>
DTA file</a> (79 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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@ -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="">2.0.0.9035</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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