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2025-04-26 14:42:58 +00:00
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reference/as.mic.html
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@ -7,7 +7,7 @@
<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="">2.1.1.9253</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9255</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">
@ -183,39 +183,31 @@
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in rbindlist(l, use.names, fill, idcol, ignore.attr):</span> Class attribute on column 5 of item 2 does not match with column 5 of item 1. You can deactivate this safety-check by using ignore.attr=TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.01</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2025</span><span style="color: #0000BB;">...</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in rbindlist(l, use.names, fill, idcol, ignore.attr):</span> Class attribute on column 5 of item 2 does not match with column 5 of item 1. You can deactivate this safety-check by using ignore.attr=TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R R R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot MIC values, see ?plot</span></span></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="as.mic-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in rbindlist(l, use.names, fill, idcol, ignore.attr):</span> Class attribute on column 4 of item 2 does not match with column 4 of item 1. You can deactivate this safety-check by using ignore.attr=TRUE</span>
<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in rbindlist(l, use.names, fill, idcol, ignore.attr):</span> Class attribute on column 4 of item 2 does not match with column 4 of item 1. You can deactivate this safety-check by using ignore.attr=TRUE</span>
<span class="r-plt img"><img src="as.mic-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># Dutch</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in rbindlist(l, use.names, fill, idcol, ignore.attr):</span> Class attribute on column 4 of item 2 does not match with column 4 of item 1. You can deactivate this safety-check by using ignore.attr=TRUE</span>
<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
</code></pre></div>
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