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(v1.4.0.9040) LA-MRSA / CA-MRSA

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dr. M.S. (Matthijs) Berends
2020-12-16 16:18:53 +01:00
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9039</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9040</span>
</span>
</div>
@ -51,14 +51,14 @@
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home"></span>
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
<span class="fas fa-question-circle"></span>
How to
@ -67,77 +67,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="articles/AMR.html">
<span class="fa fa-directions"></span>
<span class="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="articles/resistance_predict.html">
<span class="fa fa-dice"></span>
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="articles/datasets.html">
<span class="fa fa-database"></span>
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="articles/PCA.html">
<span class="fa fa-compress"></span>
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="articles/SPSS.html">
<span class="fa fa-file-upload"></span>
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="reference/mo_property.html">
<span class="fa fa-bug"></span>
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="reference/ab_property.html">
<span class="fa fa-capsules"></span>
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
@ -146,21 +146,21 @@
</li>
<li>
<a href="reference/index.html">
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Manual
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Authors
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<span class="far fa-newspaper"></span>
Changelog
</a>
@ -169,14 +169,14 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
<span class="fab fa-github"></span>
Source Code
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Survey
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@ -216,8 +216,8 @@ Since you are one of our users, we would like to know how you use the package an
<div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">
<h5 class="hasAnchor">
<a href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="anchor"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</h5>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
@ -229,7 +229,7 @@ Since you are one of our users, we would like to know how you use the package an
<span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
<span class="co">#&gt; Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), </span>
<span class="co">#&gt; 'KAN' (kanamycin), 'TOB' (tobramycin)</span>
<span class="co">#&gt; Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)</span></pre></div>
<span class="co">#&gt; Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)</span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<table class="table">
<thead><tr class="header">
@ -298,32 +298,6 @@ Since you are one of our users, we would like to know how you use the package an
</tr>
</tbody>
</table>
<div class="home-buttons">
<div class="sourceCode" id="cb2"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="sc">&lt;</span>a href<span class="ot">=</span><span class="st">"articles/datasets.html"</span><span class="sc">&gt;</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div style<span class="ot">=</span><span class="st">"background-color: #128f7635;"</span><span class="sc">&gt;</span></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div class<span class="ot">=</span><span class="st">"fa fa-database"</span><span class="sc">&gt;</span><span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>span<span class="sc">&gt;</span>Download our data sets<span class="sc">&lt;</span><span class="er">/</span>span<span class="sc">&gt;</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="er">&lt;/</span>a<span class="sc">&gt;</span></span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="er">&lt;</span>a href<span class="ot">=</span><span class="st">"articles/AMR.html"</span><span class="sc">&gt;</span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div style<span class="ot">=</span><span class="st">"background-color: #138F3865;"</span><span class="sc">&gt;</span></span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div class<span class="ot">=</span><span class="st">"fa fa-chalkboard-teacher"</span><span class="sc">&gt;</span><span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>span<span class="sc">&gt;</span>Start learning AMR analysis<span class="sc">&lt;</span><span class="er">/</span>span<span class="sc">&gt;</span></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a><span class="er">&lt;/</span>a<span class="sc">&gt;</span></span>
<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a><span class="er">&lt;</span>a href<span class="ot">=</span><span class="st">"reference/as.rsi.html"</span><span class="sc">&gt;</span></span>
<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div style<span class="ot">=</span><span class="st">"background-color: #128f7650;"</span><span class="sc">&gt;</span></span>
<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div class<span class="ot">=</span><span class="st">"fa fa-language"</span><span class="sc">&gt;</span><span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-16"><a href="#cb2-16" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>span<span class="sc">&gt;</span>Interpret MIC<span class="sc">/</span>disk values to R<span class="sc">/</span>SI<span class="sc">&lt;</span><span class="er">/</span>span<span class="sc">&gt;</span></span>
<span id="cb2-17"><a href="#cb2-17" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-18"><a href="#cb2-18" aria-hidden="true" tabindex="-1"></a><span class="er">&lt;/</span>a<span class="sc">&gt;</span></span>
<span id="cb2-19"><a href="#cb2-19" aria-hidden="true" tabindex="-1"></a><span class="er">&lt;</span>a href<span class="ot">=</span><span class="st">"articles/MDR.html"</span><span class="sc">&gt;</span></span>
<span id="cb2-20"><a href="#cb2-20" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div style<span class="ot">=</span><span class="st">"background-color: #138F3835;"</span><span class="sc">&gt;</span></span>
<span id="cb2-21"><a href="#cb2-21" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>div class<span class="ot">=</span><span class="st">"fa fa-skull-crossbones"</span><span class="sc">&gt;</span><span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-22"><a href="#cb2-22" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span>span<span class="sc">&gt;</span>Determine multi<span class="sc">-</span>drug <span class="fu">resistance</span> (MDR)<span class="sc">&lt;</span><span class="er">/</span>span<span class="sc">&gt;</span></span>
<span id="cb2-23"><a href="#cb2-23" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;/</span>div<span class="sc">&gt;</span></span>
<span id="cb2-24"><a href="#cb2-24" aria-hidden="true" tabindex="-1"></a><span class="er">&lt;/</span>a<span class="sc">&gt;</span></span></code></pre></div>
</div>
</div>
<div id="partners" class="section level4">
<h4 class="hasAnchor">
@ -365,8 +339,8 @@ Since you are one of our users, we would like to know how you use the package an
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
<p><img src="https://www.r-pkg.org/badges/version-ago/AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR"></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></pre></div>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
@ -374,9 +348,9 @@ Since you are one of our users, we would like to know how you use the package an
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p>The latest and unpublished development version can be installed from GitHub using:</p>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></pre></div>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
</div>
</div>
<div id="get-started" class="section level3">