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@ -38,7 +38,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
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|
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|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -184,9 +184,13 @@
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<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
|
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<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
|
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">oops</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <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="st">"Klebsiella"</span>, </span>
|
||||
<span> <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
|
||||
<span> ampicillin <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span></span>
|
||||
<code class="sourceCode R"><span><span class="va">oops</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||||
<span> mo <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>
|
||||
<span> <span class="st">"Klebsiella"</span>,</span>
|
||||
<span> <span class="st">"Escherichia"</span></span>
|
||||
<span> <span class="op">)</span>,</span>
|
||||
<span> ampicillin <span class="op">=</span> <span class="st">"S"</span></span>
|
||||
<span><span class="op">)</span></span>
|
||||
<span><span class="va">oops</span></span>
|
||||
<span><span class="co"># mo ampicillin</span></span>
|
||||
<span><span class="co"># 1 Klebsiella S</span></span>
|
||||
@ -198,28 +202,36 @@
|
||||
<span><span class="co"># 2 Escherichia S</span></span></code></pre></div>
|
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<p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></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="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
|
||||
<span> <span class="st">"ampicillin"</span><span class="op">)</span></span>
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
|
||||
<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="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
|
||||
<span> <span class="st">"ampicillin"</span></span>
|
||||
<span><span class="op">)</span></span>
|
||||
<span><span class="co"># [1] TRUE FALSE</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,</span>
|
||||
<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="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
|
||||
<span> <span class="st">"Klebsiella"</span>,</span>
|
||||
<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="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span></span>
|
||||
<span><span class="op">)</span></span>
|
||||
<span><span class="co"># [1] TRUE FALSE</span></span></code></pre></div>
|
||||
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
|
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<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <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="st">"Staphylococcus aureus"</span>,</span>
|
||||
<span> <span class="st">"Enterococcus faecalis"</span>,</span>
|
||||
<span> <span class="st">"Escherichia coli"</span>,</span>
|
||||
<span> <span class="st">"Klebsiella pneumoniae"</span>,</span>
|
||||
<span> <span class="st">"Pseudomonas aeruginosa"</span><span class="op">)</span>,</span>
|
||||
<span> VAN <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span></span>
|
||||
<span> AMX <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span></span>
|
||||
<span> COL <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span></span>
|
||||
<span> CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span>
|
||||
<span> CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span>
|
||||
<span> PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylenicillin</span></span>
|
||||
<span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span>
|
||||
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
|
||||
<code class="sourceCode R"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||||
<span> mo <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>
|
||||
<span> <span class="st">"Staphylococcus aureus"</span>,</span>
|
||||
<span> <span class="st">"Enterococcus faecalis"</span>,</span>
|
||||
<span> <span class="st">"Escherichia coli"</span>,</span>
|
||||
<span> <span class="st">"Klebsiella pneumoniae"</span>,</span>
|
||||
<span> <span class="st">"Pseudomonas aeruginosa"</span></span>
|
||||
<span> <span class="op">)</span>,</span>
|
||||
<span> VAN <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span></span>
|
||||
<span> AMX <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span></span>
|
||||
<span> COL <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span></span>
|
||||
<span> CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span>
|
||||
<span> CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span>
|
||||
<span> PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylenicillin</span></span>
|
||||
<span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span>
|
||||
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span>
|
||||
<span><span class="op">)</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">data</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -212,8 +212,10 @@
|
||||
<p>You can also use your own custom guideline. Custom guidelines can be set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
|
||||
<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what R considers to be the ‘formula notation’:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">custom</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,</span>
|
||||
<span> <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></span></code></pre></div>
|
||||
<code class="sourceCode R"><span><span class="va">custom</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span></span>
|
||||
<span> <span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,</span>
|
||||
<span> <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span></span>
|
||||
<span><span class="op">)</span></span></code></pre></div>
|
||||
<p>If a row/an isolate matches the first rule, the value after the first <code>~</code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The maximum number of rules is unlimited.</p>
|
||||
<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
@ -241,11 +243,11 @@
|
||||
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code> for predefined guidelines. 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>
|
||||
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains full antibiograms of 2,000 microbial isolates. It reflects reality and can be used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># to support pipes: %>%</span></span>
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># to support pipes: %>%</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span></span>
|
||||
<span><span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span></span>
|
||||
<span><span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></span></code></pre></div>
|
||||
@ -288,39 +290,43 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># random_rsi() is a helper function to generate</span></span>
|
||||
<span><span class="co"># a random vector with values S, I and R</span></span>
|
||||
<span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
|
||||
<span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||||
<span> rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
|
||||
<span><span class="op">)</span></span></code></pre></div>
|
||||
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same way:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
|
||||
<code class="sourceCode R"><span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||||
<span> RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
|
||||
<span> KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
|
||||
<span><span class="op">)</span></span></code></pre></div>
|
||||
<p>The data set now looks like this:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co"># 1 R R S R R R</span></span>
|
||||
<span><span class="co"># 2 S I S R I I</span></span>
|
||||
<span><span class="co"># 3 S I I S R R</span></span>
|
||||
<span><span class="co"># 4 S R R S I S</span></span>
|
||||
<span><span class="co"># 5 R S R S I S</span></span>
|
||||
<span><span class="co"># 6 S I S S R R</span></span>
|
||||
<span><span class="co"># 1 R R R I R R</span></span>
|
||||
<span><span class="co"># 2 R S R S R I</span></span>
|
||||
<span><span class="co"># 3 R I R R S S</span></span>
|
||||
<span><span class="co"># 4 S S I R R S</span></span>
|
||||
<span><span class="co"># 5 S S I I I R</span></span>
|
||||
<span><span class="co"># 6 S R S S I I</span></span>
|
||||
<span><span class="co"># kanamycin</span></span>
|
||||
<span><span class="co"># 1 S</span></span>
|
||||
<span><span class="co"># 2 I</span></span>
|
||||
<span><span class="co"># 3 R</span></span>
|
||||
<span><span class="co"># 4 S</span></span>
|
||||
<span><span class="co"># 5 S</span></span>
|
||||
<span><span class="co"># 6 S</span></span></code></pre></div>
|
||||
<span><span class="co"># 1 R</span></span>
|
||||
<span><span class="co"># 2 S</span></span>
|
||||
<span><span class="co"># 3 S</span></span>
|
||||
<span><span class="co"># 4 I</span></span>
|
||||
<span><span class="co"># 5 I</span></span>
|
||||
<span><span class="co"># 6 I</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
|
||||
@ -351,40 +357,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3220</td>
|
||||
<td align="right">64.40%</td>
|
||||
<td align="right">3220</td>
|
||||
<td align="right">64.40%</td>
|
||||
<td align="right">3163</td>
|
||||
<td align="right">63.26%</td>
|
||||
<td align="right">3163</td>
|
||||
<td align="right">63.26%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">986</td>
|
||||
<td align="right">19.72%</td>
|
||||
<td align="right">1043</td>
|
||||
<td align="right">20.86%</td>
|
||||
<td align="right">4206</td>
|
||||
<td align="right">84.12%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">480</td>
|
||||
<td align="right">9.60%</td>
|
||||
<td align="right">4686</td>
|
||||
<td align="right">93.72%</td>
|
||||
<td align="right">442</td>
|
||||
<td align="right">8.84%</td>
|
||||
<td align="right">4648</td>
|
||||
<td align="right">92.96%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">237</td>
|
||||
<td align="right">4.74%</td>
|
||||
<td align="right">4923</td>
|
||||
<td align="right">98.46%</td>
|
||||
<td align="right">245</td>
|
||||
<td align="right">4.90%</td>
|
||||
<td align="right">4893</td>
|
||||
<td align="right">97.86%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">77</td>
|
||||
<td align="right">1.54%</td>
|
||||
<td align="right">107</td>
|
||||
<td align="right">2.14%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -182,64 +182,65 @@
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
|
||||
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span>
|
||||
<span><span class="co"># Rows: 2,000</span></span>
|
||||
<span><span class="co"># Columns: 49</span></span>
|
||||
<span><span class="co"># $ date <span style="color: #949494; font-style: italic;"><date></span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span></span>
|
||||
<span><span class="co"># $ hospital_id <span style="color: #949494; font-style: italic;"><fct></span> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B, …</span></span>
|
||||
<span><span class="co"># $ ward_icu <span style="color: #949494; font-style: italic;"><lgl></span> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TR…</span></span>
|
||||
<span><span class="co"># $ ward_clinical <span style="color: #949494; font-style: italic;"><lgl></span> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FA…</span></span>
|
||||
<span><span class="co"># $ ward_outpatient <span style="color: #949494; font-style: italic;"><lgl></span> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…</span></span>
|
||||
<span><span class="co"># $ age <span style="color: #949494; font-style: italic;"><dbl></span> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71…</span></span>
|
||||
<span><span class="co"># $ gender <span style="color: #949494; font-style: italic;"><chr></span> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M",…</span></span>
|
||||
<span><span class="co"># $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "A77334", "A77334", "067927", "067927", "067927", "067…</span></span>
|
||||
<span><span class="co"># $ mo <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPH…</span></span>
|
||||
<span><span class="co"># $ PEN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, …</span></span>
|
||||
<span><span class="co"># $ OXA <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ FLC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, …</span></span>
|
||||
<span><span class="co"># $ AMX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span></span>
|
||||
<span><span class="co"># $ AMC <span style="color: #949494; font-style: italic;"><rsi></span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, …</span></span>
|
||||
<span><span class="co"># $ AMP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span></span>
|
||||
<span><span class="co"># $ TZP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ CZO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ FEP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ CXM <span style="color: #949494; font-style: italic;"><rsi></span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R,…</span></span>
|
||||
<span><span class="co"># $ FOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ CTX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span></span>
|
||||
<span><span class="co"># $ CAZ <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S…</span></span>
|
||||
<span><span class="co"># $ CRO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span></span>
|
||||
<span><span class="co"># $ GEN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ TOB <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA…</span></span>
|
||||
<span><span class="co"># $ AMK <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ KAN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ TMP <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R…</span></span>
|
||||
<span><span class="co"># $ SXT <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, …</span></span>
|
||||
<span><span class="co"># $ NIT <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ FOS <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ LNZ <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span></span>
|
||||
<span><span class="co"># $ CIP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, …</span></span>
|
||||
<span><span class="co"># $ MFX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ VAN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S…</span></span>
|
||||
<span><span class="co"># $ TEC <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span></span>
|
||||
<span><span class="co"># $ TCY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S…</span></span>
|
||||
<span><span class="co"># $ TGC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span></span>
|
||||
<span><span class="co"># $ DOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span></span>
|
||||
<span><span class="co"># $ ERY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span></span>
|
||||
<span><span class="co"># $ CLI <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, …</span></span>
|
||||
<span><span class="co"># $ AZM <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span></span>
|
||||
<span><span class="co"># $ IPM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span></span>
|
||||
<span><span class="co"># $ MEM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ MTR <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ CHL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ COL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R…</span></span>
|
||||
<span><span class="co"># $ MUP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ RIF <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span></span></code></pre></div>
|
||||
<span><span class="co"># Columns: 46</span></span>
|
||||
<span><span class="co"># $ date <span style="color: #949494; font-style: italic;"><date></span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2…</span></span>
|
||||
<span><span class="co"># $ patient <span style="color: #949494; font-style: italic;"><chr></span> "A77334", "A77334", "067927", "067927", "067927", "067927", "4…</span></span>
|
||||
<span><span class="co"># $ age <span style="color: #949494; font-style: italic;"><dbl></span> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50…</span></span>
|
||||
<span><span class="co"># $ gender <span style="color: #949494; font-style: italic;"><chr></span> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M", "M", "M…</span></span>
|
||||
<span><span class="co"># $ ward <span style="color: #949494; font-style: italic;"><chr></span> "Clinical", "Clinical", "ICU", "ICU", "ICU", "ICU", "Clinical"…</span></span>
|
||||
<span><span class="co"># $ mo <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPHY_EPDR",…</span></span>
|
||||
<span><span class="co"># $ PEN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,…</span></span>
|
||||
<span><span class="co"># $ OXA <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ FLC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R…</span></span>
|
||||
<span><span class="co"># $ AMX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
|
||||
<span><span class="co"># $ AMC <span style="color: #949494; font-style: italic;"><rsi></span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N…</span></span>
|
||||
<span><span class="co"># $ AMP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
|
||||
<span><span class="co"># $ TZP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ CZO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
|
||||
<span><span class="co"># $ FEP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ CXM <span style="color: #949494; font-style: italic;"><rsi></span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S…</span></span>
|
||||
<span><span class="co"># $ FOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
|
||||
<span><span class="co"># $ CTX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
|
||||
<span><span class="co"># $ CAZ <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, …</span></span>
|
||||
<span><span class="co"># $ CRO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
|
||||
<span><span class="co"># $ GEN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ TOB <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ AMK <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ KAN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ TMP <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, …</span></span>
|
||||
<span><span class="co"># $ SXT <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N…</span></span>
|
||||
<span><span class="co"># $ NIT <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,…</span></span>
|
||||
<span><span class="co"># $ FOS <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ LNZ <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
|
||||
<span><span class="co"># $ CIP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S…</span></span>
|
||||
<span><span class="co"># $ MFX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ VAN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, …</span></span>
|
||||
<span><span class="co"># $ TEC <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
|
||||
<span><span class="co"># $ TCY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, …</span></span>
|
||||
<span><span class="co"># $ TGC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
|
||||
<span><span class="co"># $ DOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
|
||||
<span><span class="co"># $ ERY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
|
||||
<span><span class="co"># $ CLI <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…</span></span>
|
||||
<span><span class="co"># $ AZM <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
|
||||
<span><span class="co"># $ IPM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
|
||||
<span><span class="co"># $ MEM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ MTR <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ CHL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ COL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …</span></span>
|
||||
<span><span class="co"># $ MUP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co"># $ RIF <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span></code></pre></div>
|
||||
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span>
|
||||
<span> genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here</span></span>
|
||||
<code class="sourceCode R"><span><span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span></span>
|
||||
<span> order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span>
|
||||
<span> genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span></span>
|
||||
<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here</span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># then get resistance of all drugs</span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, </span>
|
||||
<span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span> <span class="co"># and select only relevant columns</span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span></span>
|
||||
<span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
|
||||
<span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span>
|
||||
<span> <span class="op">)</span> <span class="co"># and select only relevant columns</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span></span>
|
||||
<span><span class="co"># <span style="color: #949494;"># A tibble: 6 × 10</span></span></span>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -162,7 +162,7 @@
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">26 August 2022</h4>
|
||||
<h4 data-toc-skip class="date">28 August 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>SPSS.Rmd</code></div>
|
||||
@ -196,7 +196,7 @@
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">460,146 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>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">461,064 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>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
||||
@ -229,9 +229,11 @@
|
||||
<span><span class="co"># [1] "Gram-negative"</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST:</span></span>
|
||||
<span><span class="va">klebsiella_test</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"klebsiella"</span>, </span>
|
||||
<span> amox <span class="op">=</span> <span class="st">"S"</span>,</span>
|
||||
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||||
<span><span class="va">klebsiella_test</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
|
||||
<span> mo <span class="op">=</span> <span class="st">"klebsiella"</span>,</span>
|
||||
<span> amox <span class="op">=</span> <span class="st">"S"</span>,</span>
|
||||
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span>
|
||||
<span><span class="op">)</span></span>
|
||||
<span><span class="va">klebsiella_test</span> <span class="co"># (our original data)</span></span>
|
||||
<span><span class="co"># mo amox</span></span>
|
||||
<span><span class="co"># 1 klebsiella S</span></span>
|
||||
@ -304,7 +306,7 @@
|
||||
<code class="sourceCode R"><span><span class="co"># download and install the latest version:</span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span></span>
|
||||
<span><span class="co"># load the package you just installed:</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org" class="external-link">haven</a></span><span class="op">)</span> </span></code></pre></div>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org" class="external-link">haven</a></span><span class="op">)</span></span></code></pre></div>
|
||||
<p>You can now import files as follows:</p>
|
||||
<div class="section level4">
|
||||
<h4 id="spss">SPSS<a class="anchor" aria-label="anchor" href="#spss"></a>
|
||||
@ -343,7 +345,7 @@
|
||||
<code class="sourceCode R"><span><span class="co"># save as regular SAS file:</span></span>
|
||||
<span><span class="fu">write_sas</span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># the SAS transport format is an open format </span></span>
|
||||
<span><span class="co"># the SAS transport format is an open format</span></span>
|
||||
<span><span class="co"># (required for submission of the data to the FDA)</span></span>
|
||||
<span><span class="fu">write_xpt</span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></span></code></pre></div>
|
||||
</div>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -183,9 +183,9 @@
|
||||
</h3>
|
||||
<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="external-link uri">https://www.tidyverse.org/</a>.</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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="co"># this package</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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="co"># this package</span></span>
|
||||
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></span></code></pre></div>
|
||||
<p>We will have to transform some variables to simplify and automate the analysis:</p>
|
||||
<ul>
|
||||
@ -196,7 +196,7 @@
|
||||
<code class="sourceCode R"><span><span class="co"># transform variables</span></span>
|
||||
<span><span class="va">data</span> <span class="op"><-</span> <span class="va">WHONET</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="co"># get microbial ID based on given organism</span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>No errors or warnings, so all values are transformed succesfully.</p>
|
||||
@ -363,7 +363,7 @@ Drug group: Beta-lactams/penicillins<br>
|
||||
<code class="sourceCode R"><span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">Country</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">'ab'</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
|
||||
<span> <span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">"ab"</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
|
||||
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -161,7 +161,7 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">26 August 2022</h4>
|
||||
<h4 data-toc-skip class="date">28 August 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
@ -177,7 +177,7 @@
|
||||
</h2>
|
||||
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.3 MB)<br>
|
||||
@ -403,7 +403,7 @@
|
||||
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
|
||||
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
|
||||
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">original R Data Structure (RDS) file</a> (0.2 MB)<br>
|
||||
@ -473,18 +473,18 @@
|
||||
</h2>
|
||||
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
||||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated text file</a> (0.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated text file</a> (0.2 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft Excel workbook</a> (65 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft Excel workbook</a> (66 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache Feather file</a> (98 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache Feather file</a> (97 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache Parquet file</a> (76 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache Parquet file</a> (74 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS data file</a> (1.8 MB)<br>
|
||||
</li>
|
||||
@ -646,7 +646,7 @@
|
||||
</h2>
|
||||
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
|
||||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
|
||||
@ -655,13 +655,13 @@
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Microsoft Excel workbook</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache Feather file</a> (13 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache Feather file</a> (12 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache Parquet file</a> (11 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache Parquet file</a> (10 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS data file</a> (80 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM SPSS Statistics data file</a> (68 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM SPSS Statistics data file</a> (27 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata DTA file</a> (67 kB)</li>
|
||||
</ul>
|
||||
@ -778,7 +778,7 @@
|
||||
</h2>
|
||||
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
|
||||
@ -789,7 +789,7 @@
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.feather" class="external-link">Apache Feather file</a> (0.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache Parquet file</a> (0.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache Parquet file</a> (99 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS data file</a> (4 MB)<br>
|
||||
</li>
|
||||
@ -937,7 +937,7 @@
|
||||
</h2>
|
||||
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
|
||||
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
|
||||
@ -1209,7 +1209,7 @@
|
||||
</h2>
|
||||
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
|
||||
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
|
||||
@ -1218,13 +1218,13 @@
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Microsoft Excel workbook</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache Feather file</a> (12 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache Feather file</a> (11 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache Parquet file</a> (8 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache Parquet file</a> (7 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS data file</a> (52 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM SPSS Statistics data file</a> (45 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM SPSS Statistics data file</a> (23 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata DTA file</a> (44 kB)</li>
|
||||
</ul>
|
||||
@ -1319,6 +1319,502 @@
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="example_isolates-example-data-for-practice">
|
||||
<code>example_isolates</code>: Example Data for Practice<a class="anchor" aria-label="anchor" href="#example_isolates-example-data-for-practice"></a>
|
||||
</h2>
|
||||
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
|
||||
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
|
||||
</h3>
|
||||
<p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-7">Example content<a class="anchor" aria-label="anchor" href="#example-content-7"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="4%">
|
||||
<col width="3%">
|
||||
<col width="1%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="5%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
<col width="1%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">date</th>
|
||||
<th align="center">patient</th>
|
||||
<th align="center">age</th>
|
||||
<th align="center">gender</th>
|
||||
<th align="center">ward</th>
|
||||
<th align="center">mo</th>
|
||||
<th align="center">PEN</th>
|
||||
<th align="center">OXA</th>
|
||||
<th align="center">FLC</th>
|
||||
<th align="center">AMX</th>
|
||||
<th align="center">AMC</th>
|
||||
<th align="center">AMP</th>
|
||||
<th align="center">TZP</th>
|
||||
<th align="center">CZO</th>
|
||||
<th align="center">FEP</th>
|
||||
<th align="center">CXM</th>
|
||||
<th align="center">FOX</th>
|
||||
<th align="center">CTX</th>
|
||||
<th align="center">CAZ</th>
|
||||
<th align="center">CRO</th>
|
||||
<th align="center">GEN</th>
|
||||
<th align="center">TOB</th>
|
||||
<th align="center">AMK</th>
|
||||
<th align="center">KAN</th>
|
||||
<th align="center">TMP</th>
|
||||
<th align="center">SXT</th>
|
||||
<th align="center">NIT</th>
|
||||
<th align="center">FOS</th>
|
||||
<th align="center">LNZ</th>
|
||||
<th align="center">CIP</th>
|
||||
<th align="center">MFX</th>
|
||||
<th align="center">VAN</th>
|
||||
<th align="center">TEC</th>
|
||||
<th align="center">TCY</th>
|
||||
<th align="center">TGC</th>
|
||||
<th align="center">DOX</th>
|
||||
<th align="center">ERY</th>
|
||||
<th align="center">CLI</th>
|
||||
<th align="center">AZM</th>
|
||||
<th align="center">IPM</th>
|
||||
<th align="center">MEM</th>
|
||||
<th align="center">MTR</th>
|
||||
<th align="center">CHL</th>
|
||||
<th align="center">COL</th>
|
||||
<th align="center">MUP</th>
|
||||
<th align="center">RIF</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2002-01-02</td>
|
||||
<td align="center">A77334</td>
|
||||
<td align="center">65</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Clinical</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">I</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">I</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2002-01-03</td>
|
||||
<td align="center">A77334</td>
|
||||
<td align="center">65</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Clinical</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">I</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">I</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2002-01-07</td>
|
||||
<td align="center">067927</td>
|
||||
<td align="center">45</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">ICU</td>
|
||||
<td align="center">B_STPHY_EPDR</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></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"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2002-01-07</td>
|
||||
<td align="center">067927</td>
|
||||
<td align="center">45</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">ICU</td>
|
||||
<td align="center">B_STPHY_EPDR</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></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"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2002-01-13</td>
|
||||
<td align="center">067927</td>
|
||||
<td align="center">45</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">ICU</td>
|
||||
<td align="center">B_STPHY_EPDR</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2002-01-13</td>
|
||||
<td align="center">067927</td>
|
||||
<td align="center">45</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">ICU</td>
|
||||
<td align="center">B_STPHY_EPDR</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">R</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="example_isolates_unclean-example-data-for-practice">
|
||||
<code>example_isolates_unclean</code>: Example Data for Practice<a class="anchor" aria-label="anchor" href="#example_isolates_unclean-example-data-for-practice"></a>
|
||||
</h2>
|
||||
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
|
||||
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
|
||||
</h3>
|
||||
<p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-8">Example content<a class="anchor" aria-label="anchor" href="#example-content-8"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">patient_id</th>
|
||||
<th align="center">hospital</th>
|
||||
<th align="center">date</th>
|
||||
<th align="center">bacteria</th>
|
||||
<th align="center">AMX</th>
|
||||
<th align="center">AMC</th>
|
||||
<th align="center">CIP</th>
|
||||
<th align="center">GEN</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">J3</td>
|
||||
<td align="center">A</td>
|
||||
<td align="center">2012-11-21</td>
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">R7</td>
|
||||
<td align="center">A</td>
|
||||
<td align="center">2018-04-03</td>
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">P3</td>
|
||||
<td align="center">A</td>
|
||||
<td align="center">2014-09-19</td>
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">P10</td>
|
||||
<td align="center">A</td>
|
||||
<td align="center">2015-12-10</td>
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">B7</td>
|
||||
<td align="center">A</td>
|
||||
<td align="center">2015-03-02</td>
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">W3</td>
|
||||
<td align="center">A</td>
|
||||
<td align="center">2018-03-31</td>
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
</nav></aside>
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -186,55 +186,42 @@
|
||||
</h2>
|
||||
<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>
|
||||
<p>It is basically as easy as:</p>
|
||||
<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>
|
||||
<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>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># or:</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> model <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>predict_TZP <span class="ot"><-</span> example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
<span><span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>tbl <span class="op">=</span> <span class="va">example_isolates</span>, col_date <span class="op">=</span> <span class="st">"date"</span>, col_ab <span class="op">=</span> <span class="st">"TZP"</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># or:</span></span>
|
||||
<span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span></span>
|
||||
<span> col_ab <span class="op">=</span> <span class="st">"TZP"</span>,</span>
|
||||
<span> model <span class="op">=</span> <span class="st">"binomial"</span></span>
|
||||
<span> <span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span><span class="va">predict_TZP</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span></span>
|
||||
<span> col_ab <span class="op">=</span> <span class="st">"TZP"</span>,</span>
|
||||
<span> model <span class="op">=</span> <span class="st">"binomial"</span></span>
|
||||
<span> <span class="op">)</span></span></code></pre></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
|
||||
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">predict_TZP</span></span>
|
||||
<span><span class="co"># year value se_min se_max observations observed estimated</span></span>
|
||||
<span><span class="co"># 1 2002 0.20000000 NA NA 15 0.20000000 0.05616378</span></span>
|
||||
<span><span class="co"># 2 2003 0.06250000 NA NA 32 0.06250000 0.06163839</span></span>
|
||||
<span><span class="co"># 3 2004 0.08536585 NA NA 82 0.08536585 0.06760841</span></span>
|
||||
<span><span class="co"># 4 2005 0.05000000 NA NA 60 0.05000000 0.07411100</span></span>
|
||||
<span><span class="co"># 5 2006 0.05084746 NA NA 59 0.05084746 0.08118454</span></span>
|
||||
<span><span class="co"># 6 2007 0.12121212 NA NA 66 0.12121212 0.08886843</span></span>
|
||||
<span><span class="co"># 7 2008 0.04166667 NA NA 72 0.04166667 0.09720264</span></span>
|
||||
<span><span class="co"># 8 2009 0.01639344 NA NA 61 0.01639344 0.10622731</span></span>
|
||||
<span><span class="co"># 9 2010 0.05660377 NA NA 53 0.05660377 0.11598223</span></span>
|
||||
<span><span class="co"># 10 2011 0.18279570 NA NA 93 0.18279570 0.12650615</span></span>
|
||||
<span><span class="co"># 11 2012 0.30769231 NA NA 65 0.30769231 0.13783610</span></span>
|
||||
<span><span class="co"># 12 2013 0.06896552 NA NA 58 0.06896552 0.15000651</span></span>
|
||||
<span><span class="co"># 13 2014 0.10000000 NA NA 60 0.10000000 0.16304829</span></span>
|
||||
<span><span class="co"># 14 2015 0.23636364 NA NA 55 0.23636364 0.17698785</span></span>
|
||||
<span><span class="co"># 15 2016 0.22619048 NA NA 84 0.22619048 0.19184597</span></span>
|
||||
<span><span class="co"># 16 2017 0.16279070 NA NA 86 0.16279070 0.20763675</span></span>
|
||||
<span><span class="co"># 17 2018 0.22436641 0.1938710 0.2548618 NA NA 0.22436641</span></span>
|
||||
<span><span class="co"># 18 2019 0.24203228 0.2062911 0.2777735 NA NA 0.24203228</span></span>
|
||||
<span><span class="co"># 19 2020 0.26062172 0.2191758 0.3020676 NA NA 0.26062172</span></span>
|
||||
<span><span class="co"># 20 2021 0.28011130 0.2325557 0.3276669 NA NA 0.28011130</span></span>
|
||||
<span><span class="co"># 21 2022 0.30046606 0.2464567 0.3544755 NA NA 0.30046606</span></span>
|
||||
<span><span class="co"># 22 2023 0.32163907 0.2609011 0.3823771 NA NA 0.32163907</span></span>
|
||||
<span><span class="co"># 23 2024 0.34357130 0.2759081 0.4112345 NA NA 0.34357130</span></span>
|
||||
<span><span class="co"># 24 2025 0.36619175 0.2914934 0.4408901 NA NA 0.36619175</span></span>
|
||||
<span><span class="co"># 25 2026 0.38941799 0.3076686 0.4711674 NA NA 0.38941799</span></span>
|
||||
<span><span class="co"># 26 2027 0.41315710 0.3244399 0.5018743 NA NA 0.41315710</span></span>
|
||||
<span><span class="co"># 27 2028 0.43730688 0.3418075 0.5328063 NA NA 0.43730688</span></span>
|
||||
<span><span class="co"># 28 2029 0.46175755 0.3597639 0.5637512 NA NA 0.46175755</span></span>
|
||||
<span><span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span></span>
|
||||
<span><span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span></span>
|
||||
<span><span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></span></code></pre></div>
|
||||
<span><span class="co"># <span style="color: #949494;"># A tibble: 31 × 7</span></span></span>
|
||||
<span><span class="co"># year value se_min se_max observations observed estimated</span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 1</span> <span style="text-decoration: underline;">2</span>002 0.2 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 15 0.2 0.056<span style="text-decoration: underline;">2</span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 2</span> <span style="text-decoration: underline;">2</span>003 0.062<span style="text-decoration: underline;">5</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 32 0.062<span style="text-decoration: underline;">5</span> 0.061<span style="text-decoration: underline;">6</span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 3</span> <span style="text-decoration: underline;">2</span>004 0.085<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 82 0.085<span style="text-decoration: underline;">4</span> 0.067<span style="text-decoration: underline;">6</span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 4</span> <span style="text-decoration: underline;">2</span>005 0.05 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 60 0.05 0.074<span style="text-decoration: underline;">1</span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 5</span> <span style="text-decoration: underline;">2</span>006 0.050<span style="text-decoration: underline;">8</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 59 0.050<span style="text-decoration: underline;">8</span> 0.081<span style="text-decoration: underline;">2</span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 6</span> <span style="text-decoration: underline;">2</span>007 0.121 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 66 0.121 0.088<span style="text-decoration: underline;">9</span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 7</span> <span style="text-decoration: underline;">2</span>008 0.041<span style="text-decoration: underline;">7</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 72 0.041<span style="text-decoration: underline;">7</span> 0.097<span style="text-decoration: underline;">2</span></span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 8</span> <span style="text-decoration: underline;">2</span>009 0.016<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 61 0.016<span style="text-decoration: underline;">4</span> 0.106 </span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;"> 9</span> <span style="text-decoration: underline;">2</span>010 0.056<span style="text-decoration: underline;">6</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 53 0.056<span style="text-decoration: underline;">6</span> 0.116 </span></span>
|
||||
<span><span class="co"># <span style="color: #BCBCBC;">10</span> <span style="text-decoration: underline;">2</span>011 0.183 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 93 0.183 0.127 </span></span>
|
||||
<span><span class="co"># <span style="color: #949494;"># … with 21 more rows</span></span></span></code></pre></div>
|
||||
<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>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><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></span></code></pre></div>
|
||||
@ -256,7 +243,7 @@
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
|
||||
@ -302,7 +289,7 @@
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -171,7 +171,6 @@
|
||||
<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
|
||||
<hr>
|
||||
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p><img src="AMR_intro.png" width="555px"></p>
|
||||
<p>After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>The <code>AMR</code> package is available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
||||
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
|
||||
|
||||
Reference in New Issue
Block a user