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14
articles/AMR.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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@ -205,7 +205,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 13 June 2024.</p>
generated on 14 June 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-06-13</td>
<td align="center">2024-06-14</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2024-06-13</td>
<td align="center">2024-06-14</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2024-06-13</td>
<td align="center">2024-06-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -579,14 +579,14 @@ impression, as it comes with support for the new <code>mo</code> and
<span><span class="co">#&gt; Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.1% (n=437) %I :12.0% (n=325) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.9% (n=1163) %R :36.1% (n=978) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %N : 0.0% (n=0) %N : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; CIP GEN first </span></span>
<span><span class="co">#&gt; Class:sir Class:sir Mode:logical </span></span>
<span><span class="co">#&gt; %S :51.5% (n=1396) %S :59.6% (n=1616) TRUE:2712 </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 6.6% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1138) %R :37.3% (n=1011) </span></span>
<span><span class="co">#&gt; %N : 0.0% (n=0) %N : 0.0% (n=0)</span></span></code></pre></div>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span></code></pre></div>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>

2
articles/EUCAST.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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articles/MDR.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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2
articles/PCA.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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articles/WHONET.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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@ -372,7 +372,7 @@ Longest: 40</p>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; sir (numeric)<br>
Length: 500<br>
Levels: 5: S &lt; SDD &lt; I &lt; R &lt; N<br>
Levels: 5: S &lt; SDD &lt; I &lt; R &lt; NI<br>
Available: 481 (96.2%, NA: 19 = 3.8%)<br>
Unique: 3</p>
<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02)<br>

48
articles/datasets.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</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">
@ -194,7 +194,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">13 June 2024</h4>
<h4 data-toc-skip class="date">14 June 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -526,14 +526,14 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<h2 id="antibiotics-antibiotic-antifungal-drugs">
<code>antibiotics</code>: Antibiotic (+Antifungal) Drugs<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-antifungal-drugs"></a>
</h2>
<p>A data set with 484 rows and 14 columns, containing the following
<p>A data set with 485 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 13 June 2024 18:55:17 UTC. Find more info
<p>It was last updated on 14 June 2024 20:39:01 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -905,47 +905,47 @@ 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 29 883 rows and 13 columns, containing the following
<p>A data set with 34 085 rows and 13 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>host</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 24 February 2024 14:16:52 UTC. Find more info
<p>It was last updated on 14 June 2024 20:39:01 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (61 kB)<br>
R Data Structure (RDS) file</a> (71 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> (2.5 MB)<br>
text file</a> (2.9 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> (1.4 MB)<br>
Excel workbook</a> (1.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (1.3 MB)<br>
Feather file</a> (4.9 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> (91 kB)<br>
Parquet file</a> (0 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> (8.2 MB)<br>
transport (XPT) file</a> (9.3 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> (4.9 MB)<br>
SPSS Statistics data file</a> (5.6 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> (8.1 MB)</li>
DTA file</a> (9.2 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk
diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
(2011-2023).</p>
diffusion diameters. Included guidelines are CLSI (2011-2024) and EUCAST
(2011-2024).</p>
<p>Clinical breakpoints in this package were validated through and
imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop
Windows application developed and supported by the WHO Collaborating
@ -1007,7 +1007,7 @@ use.</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -1024,7 +1024,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -1041,7 +1041,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -1058,7 +1058,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -1075,7 +1075,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -1092,7 +1092,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -2176,11 +2176,11 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
<h2 id="microorganisms-codes-common-laboratory-codes">
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
</h2>
<p>A data set with 4 958 rows and 2 columns, containing the following
<p>A data set with 4 972 rows and 2 columns, containing the following
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 13 June 2024 05:37:53 UTC. Find more info
<p>It was last updated on 14 June 2024 20:39:01 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>

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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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articles/other_pkg.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/resistance_predict.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/welcome_to_AMR.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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