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(v1.3.0.9001) website update
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@ -82,7 +82,7 @@
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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="Latest development version">1.3.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
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</span>
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</div>
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@ -236,25 +236,25 @@
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</div>
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<pre class="usage"><span class='fu'>mdro</span>(
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<span class='no'>x</span>,
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<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CMI2012"</span>,
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<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
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<span class='kw'>pct_required_classes</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
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<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='no'>...</span>
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<span class='kw'>x</span>,
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guideline = <span class='st'>"CMI2012"</span>,
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col_mo = <span class='kw'>NULL</span>,
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info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
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pct_required_classes = <span class='fl'>0.5</span>,
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combine_SI = <span class='fl'>TRUE</span>,
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verbose = <span class='fl'>FALSE</span>,
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<span class='kw'>...</span>
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)
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<span class='fu'>brmo</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"BRMO"</span>, <span class='no'>...</span>)
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<span class='fu'>brmo</span>(<span class='kw'>x</span>, guideline = <span class='st'>"BRMO"</span>, <span class='kw'>...</span>)
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<span class='fu'>mrgn</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"MRGN"</span>, <span class='no'>...</span>)
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<span class='fu'>mrgn</span>(<span class='kw'>x</span>, guideline = <span class='st'>"MRGN"</span>, <span class='kw'>...</span>)
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<span class='fu'>mdr_tb</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"TB"</span>, <span class='no'>...</span>)
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<span class='fu'>mdr_tb</span>(<span class='kw'>x</span>, guideline = <span class='st'>"TB"</span>, <span class='kw'>...</span>)
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<span class='fu'>mdr_cmi2012</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CMI2012"</span>, <span class='no'>...</span>)
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<span class='fu'>mdr_cmi2012</span>(<span class='kw'>x</span>, guideline = <span class='st'>"CMI2012"</span>, <span class='kw'>...</span>)
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<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
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<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='kw'>x</span>, guideline = <span class='st'>"EUCAST"</span>, <span class='kw'>...</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -440,18 +440,18 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>cleaner</span>)
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<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</span>) {
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://github.com/msberends/cleaner'>cleaner</a></span>)
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<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'>mdro</span>() <span class='kw'>%>%</span>
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'>mdro</span>() <span class='op'>%>%</span>
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<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>()
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<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>.</span>),
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<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>),
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<span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))
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<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(EUCAST = <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='kw'>.</span>),
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BRMO = <span class='fu'>brmo</span>(<span class='kw'>.</span>),
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MRGN = <span class='fu'>mrgn</span>(<span class='kw'>.</span>))
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}</pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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@ -468,7 +468,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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</div>
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</footer>
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