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(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement
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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">1.5.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9014</span>
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</span>
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</div>
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@ -271,7 +271,7 @@
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<h3 class="hasAnchor">
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<a href="#examples" class="anchor"></a>Examples</h3>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
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<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
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<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><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="co"># to support pipes: %>%</span>
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<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://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
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@ -339,17 +339,17 @@ Unique: 2</p>
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
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<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
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<span class="co"># 1 R I I R R R</span>
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<span class="co"># 2 R S I S R S</span>
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<span class="co"># 3 R R S S R I</span>
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<span class="co"># 4 S R R S S R</span>
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<span class="co"># 5 I R R R R S</span>
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<span class="co"># 6 I I I R S I</span>
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<span class="co"># 1 I R R I I S</span>
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<span class="co"># 2 I S R I R R</span>
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<span class="co"># 3 S I S I S S</span>
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<span class="co"># 4 S R I S S S</span>
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<span class="co"># 5 I S I R S S</span>
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<span class="co"># 6 S R I R S S</span>
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<span class="co"># kanamycin</span>
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<span class="co"># 1 I</span>
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<span class="co"># 1 S</span>
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<span class="co"># 2 S</span>
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<span class="co"># 3 S</span>
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<span class="co"># 4 S</span>
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<span class="co"># 3 R</span>
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<span class="co"># 4 I</span>
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<span class="co"># 5 R</span>
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<span class="co"># 6 R</span></code></pre></div>
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<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
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@ -382,40 +382,40 @@ Unique: 5</p>
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<tr class="odd">
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<td align="left">1</td>
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<td align="left">Mono-resistant</td>
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<td align="right">3163</td>
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<td align="right">63.26%</td>
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<td align="right">3163</td>
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<td align="right">63.26%</td>
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<td align="right">3211</td>
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<td align="right">64.22%</td>
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<td align="right">3211</td>
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<td align="right">64.22%</td>
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</tr>
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<tr class="even">
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<td align="left">2</td>
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<td align="left">Negative</td>
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<td align="right">1009</td>
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<td align="right">20.18%</td>
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<td align="right">4172</td>
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<td align="right">83.44%</td>
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<td align="right">990</td>
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<td align="right">19.80%</td>
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<td align="right">4201</td>
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<td align="right">84.02%</td>
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</tr>
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<tr class="odd">
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<td align="left">3</td>
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<td align="left">Multi-drug-resistant</td>
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<td align="right">466</td>
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<td align="right">9.32%</td>
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<td align="right">4638</td>
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<td align="right">92.76%</td>
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<td align="right">435</td>
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<td align="right">8.70%</td>
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<td align="right">4636</td>
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<td align="right">92.72%</td>
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</tr>
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<tr class="even">
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<td align="left">4</td>
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<td align="left">Poly-resistant</td>
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<td align="right">255</td>
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<td align="right">5.10%</td>
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<td align="right">4893</td>
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<td align="right">97.86%</td>
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<td align="right">258</td>
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<td align="right">5.16%</td>
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<td align="right">4894</td>
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<td align="right">97.88%</td>
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</tr>
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<tr class="odd">
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<td align="left">5</td>
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<td align="left">Extensively drug-resistant</td>
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<td align="right">107</td>
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<td align="right">2.14%</td>
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<td align="right">106</td>
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<td align="right">2.12%</td>
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<td align="right">5000</td>
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<td align="right">100.00%</td>
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</tr>
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@ -39,7 +39,7 @@
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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">1.5.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9014</span>
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</span>
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</div>
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@ -193,7 +193,7 @@
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<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">28 January 2021</h4>
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<h4 class="date">02 February 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
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<div class="hidden name"><code>SPSS.Rmd</code></div>
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@ -228,7 +228,7 @@
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</li>
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<li>
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<p><strong>R has a huge community.</strong></p>
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<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">384,445 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
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<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">385,525 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
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</li>
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<li>
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<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
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@ -81,7 +81,7 @@
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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">1.5.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9014</span>
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</span>
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</div>
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@ -240,7 +240,7 @@
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<p class="section-desc"></p>
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<dl>
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<dt><a href="AMR.html">How to conduct AMR analysis</a></dt>
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<dt><a href="AMR.html">How to conduct AMR data analysis</a></dt>
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<dd></dt>
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<dt><a href="EUCAST.html">How to apply EUCAST rules</a></dt>
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<dd></dt>
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@ -39,7 +39,7 @@
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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">1.5.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9014</span>
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</span>
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</div>
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@ -203,7 +203,7 @@
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<div id="needed-r-packages" class="section level2">
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<h2 class="hasAnchor">
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<a href="#needed-r-packages" class="anchor"></a>Needed R packages</h2>
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<p>As with many uses in R, we need some additional packages for AMR analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
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<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
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<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><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>
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@ -216,7 +216,7 @@
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<div id="prediction-analysis" class="section level2">
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<h2 class="hasAnchor">
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<a href="#prediction-analysis" class="anchor"></a>Prediction analysis</h2>
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<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
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<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
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<p>It is basically as easy as:</p>
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<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="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
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<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
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@ -265,7 +265,8 @@
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<span class="co"># 26 2027 0.41315710 0.3244399 0.5018743 NA NA 0.41315710</span>
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<span class="co"># 27 2028 0.43730688 0.3418075 0.5328063 NA NA 0.43730688</span>
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<span class="co"># 28 2029 0.46175755 0.3597639 0.5637512 NA NA 0.46175755</span>
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<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span></code></pre></div>
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<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span>
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<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span></code></pre></div>
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<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
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<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
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@ -39,7 +39,7 @@
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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">1.5.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9014</span>
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</span>
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</div>
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@ -216,7 +216,7 @@
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<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
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<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</li>
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<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</li>
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<li>Determining first isolates to be used for AMR analysis</li>
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<li>Determining first isolates to be used for AMR data analysis</li>
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<li>Calculating antimicrobial resistance</li>
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<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</li>
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<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies</li>
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