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(v1.4.0.9034) MIC printing update

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dr. M.S. (Matthijs) Berends
2020-12-09 09:40:50 +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">1.4.0.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9034</span>
</span>
</div>
@ -214,109 +214,103 @@ Since you are one of our users, we would like to know how you use the package an
</p>
<br><br>
</div>
<div id="with-amr-for-r-youll-always-have-a-knowledgeable-microbiologist-at-your-side" class="section level5">
<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-youll-always-have-a-knowledgeable-microbiologist-at-your-side" class="anchor"></a>With <code>AMR</code> (for R), you’ll always have a knowledgeable microbiologist at 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>
<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>
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">glycopeptides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_gram_positive()</span>
<span class="co">#&gt; Selecting cephalosporins: 'CAZ' (ceftazidime), 'CRO' (ceftriaxone),</span>
<span class="co">#&gt; 'CTX' (cefotaxime), 'CXM' (cefuroxime), </span>
<span class="co">#&gt; 'CZO' (cefazolin), 'FEP' (cefepime),</span>
<span class="co">#&gt; 'FOX' (cefoxitin)</span>
<span class="co">#&gt; Selecting glycopeptides: 'TEC' (teicoplanin), 'VAN' (vancomycin)</span></pre></div>
<p>With only having defined a filter on Gram-positive micro-organisms (<code><a href="reference/mo_property.html">mo_is_gram_positive()</a></code>) and a selection of two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">glycopeptides()</a></code>), the reference data about <a href="./reference/microorganisms.html">all bugs</a> and <a href="./reference/antibiotics.html">drugs</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<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="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="kw">library</span>(AMR)</span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="kw">library</span>(dplyr)</span>
<span id="cb1-4"><a href="#cb1-4"></a></span>
<span id="cb1-5"><a href="#cb1-5"></a>example_isolates <span class="op">%&gt;%</span></span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">mo =</span> <span class="kw">mo_fullname</span>(mo)) <span class="op">%&gt;%</span></span>
<span id="cb1-7"><a href="#cb1-7"></a><span class="st"> </span><span class="kw">filter</span>(<span class="kw">mo_is_gram_negative</span>(), <span class="kw">mo_is_intrinsic_resistant</span>(<span class="dt">ab =</span> <span class="st">"cefotax"</span>)) <span class="op">%&gt;%</span></span>
<span id="cb1-8"><a href="#cb1-8"></a><span class="st"> </span><span class="kw">select</span>(mo, <span class="kw">aminoglycosides</span>(), <span class="kw">carbapenems</span>())</span>
<span id="cb1-9"><a href="#cb1-9"></a><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column 'mo' as input for mo_is_gram_negative()</span></span>
<span id="cb1-10"><a href="#cb1-10"></a><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column 'mo' as input for mo_is_intrinsic_resistant()</span></span>
<span id="cb1-11"><a href="#cb1-11"></a><span class="co">#&gt; Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), </span></span>
<span id="cb1-12"><a href="#cb1-12"></a> <span class="st">'KAN'</span> (kanamycin), <span class="st">'TOB'</span> (tobramycin)</span>
<span id="cb1-13"><a href="#cb1-13"></a><span class="co">#&gt; Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)</span></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_positive()</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">
<th align="left">mo</th>
<th align="center">CAZ</th>
<th align="center">CRO</th>
<th align="center">CTX</th>
<th align="center">CXM</th>
<th align="center">CZO</th>
<th align="center">FEP</th>
<th align="center">FOX</th>
<th align="center">TEC</th>
<th align="center">VAN</th>
<th align="center">AMK</th>
<th align="center">GEN</th>
<th align="center">KAN</th>
<th align="center">TOB</th>
<th align="center">IPM</th>
<th align="center">MEM</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left"><em>Enterococcus faecalis</em></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="left"><em>Enterococcus faecalis</em></td>
<td align="center">R</td>
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="left"><em>Enterococcus faecalis</em></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="left">
<em>Streptococcus</em> group B</td>
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Staphylococcus epidermidis</em></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left"><em>Enterococcus faecium</em></td>
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Stenotrophomonas maltophilia</em></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
@ -462,7 +456,7 @@ Since you are one of our users, we would like to know how you use the package an
<li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>)</li>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise()</code>)</li>
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
</ul>