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big website update, licence txt update
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@ -49,7 +49,7 @@
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<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
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<meta property="og:image" content="https://msberends.gitlab.io/logo.png" />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary" />
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9008</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
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</span>
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</div>
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@ -93,12 +93,65 @@
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Home
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</a>
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</li>
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<li>
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<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fa fa-question-circle"></span>
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Get Started
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How to
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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Conduct AMR analysis
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</a>
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</li>
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<li>
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<a href="../articles/Predict.html">
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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</a>
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</li>
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<li>
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<a href="../articles/EUCAST.html">
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<span class="fa fa-exchange-alt"></span>
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Apply EUCAST rules
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</a>
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</li>
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<li>
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<a href="../articles/mo_property.html">
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<span class="fa fa-bug"></span>
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Get properties of a microorganism
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</a>
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</li>
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<li>
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<a href="../articles/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antibiotic
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</a>
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</li>
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<li>
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<a href="../articles/freq.html">
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<span class="fa fa-sort-amount-down"></span>
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Create frequency tables
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</a>
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</li>
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<li>
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<a href="../articles/G_test.html">
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<span class="fa fa-clipboard-check"></span>
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Use the G-test
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</a>
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</li>
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</ul>
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</li>
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<li>
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<a href="../reference/">
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@ -121,17 +174,17 @@
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Changelog
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</a>
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</li>
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<li>
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</ul>
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<ul class="nav navbar-nav navbar-right">
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<li>
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<a href="https://gitlab.com/msberends/AMR">
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<span class="fab fa fab fa-gitlab"></span>
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Source Code
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</a>
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</li>
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</ul>
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<ul class="nav navbar-nav navbar-right">
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<li>
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<li>
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<a href="../LICENSE-text.html">
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<span class="fa fa-book"></span>
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@ -188,31 +241,29 @@
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<p>Ordered factor with new class <code>mic</code></p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi</a></code></p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><div class='input'><span class='no'>mic_data</span> <span class='kw'><-</span> <span class='fu'>as.mic</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>">=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"<=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span>))
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<span class='fu'>is.mic</span>(<span class='no'>mic_data</span>)</div><div class='output co'>#> [1] TRUE</div><div class='input'>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='no'>mic_data</span> <span class='kw'><-</span> <span class='fu'>as.mic</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>">=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"<=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span>))
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<span class='fu'>is.mic</span>(<span class='no'>mic_data</span>)
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<span class='co'># this can also coerce combined MIC/RSI values:</span>
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<span class='fu'>as.mic</span>(<span class='st'>"<=0.002; S"</span>) <span class='co'># will return <=0.002</span></div><div class='output co'>#> Class 'mic'
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#> [1] <=0.002</div><div class='input'>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>mic_data</span>)</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>mic_data</span>)</div><div class='img'><img src='as.mic-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>mic_data</span>)</div><div class='output co'>#>
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#>
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#> **Frequency table**
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#>
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#>
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#> | |Item | Count| Percent| Cum. Count| Cum. Percent|
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#> |:--|:-------|-----:|-------:|----------:|------------:|
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#> |1 |1 | 3| 33.3%| 3| 33.3%|
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#> |2 |8 | 2| 22.2%| 5| 55.6%|
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#> |3 |16 | 2| 22.2%| 7| 77.8%|
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#> |4 |<=0.128 | 1| 11.1%| 8| 88.9%|
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#> |5 |>=32 | 1| 11.1%| 9| 100.0%|
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#>
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#> </div></pre>
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<span class='fu'>as.mic</span>(<span class='st'>"<=0.002; S"</span>) <span class='co'># will return <=0.002</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>mic_data</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>mic_data</span>)
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<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>mic_data</span>)
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
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@ -221,6 +272,8 @@
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<li><a href="#value">Value</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#see-also">See also</a></li>
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<li><a href="#examples">Examples</a></li>
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