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dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
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commit 7d16bec21f
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR
Version: 1.3.0.9000
Version: 1.3.0.9001
Date: 2020-08-10
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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# AMR 1.3.0.9000
# AMR 1.3.0.9001
## <small>Last updated: 10 August 2020</small>
### Changed

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R/rsi.R
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#' library(dplyr)
#' df %>% mutate_at(vars(AMP:TOB), as.rsi)
#' df %>% mutate(across(AMP:TOB), as.rsi)
#'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
#'

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docs/404.html
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@@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -248,7 +248,7 @@ Content not found. Please use links in the navbar.
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/LICENSE-text.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -496,7 +496,7 @@ END OF TERMS AND CONDITIONS
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

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docs/articles/AMR.html
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docs/articles/EUCAST.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -186,7 +186,7 @@
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div>
@@ -209,33 +209,39 @@
<a href="#examples" class="anchor"></a>Examples</h2>
<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>
<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>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">oops</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>,
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="kw">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(mo = <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>,
<span class="st">"Escherichia"</span>),
<span class="kw">ampicillin</span> <span class="kw">=</span> <span class="st">"S"</span>)
<span class="no">oops</span>
ampicillin = <span class="st">"S"</span>)
<span class="kw">oops</span>
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella S</span>
<span class="co"># 2 Escherichia S</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">oops</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">oops</span>, info = <span class="fl">FALSE</span>)
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella R</span>
<span class="co"># 2 Escherichia S</span></pre></body></html></div>
<span class="co"># 2 Escherichia S</span>
</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> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(mo = <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,
<span class="st">"Enterococcus faecalis"</span>,
<span class="st">"Escherichia coli"</span>,
<span class="st">"Klebsiella pneumoniae"</span>,
<span class="st">"Pseudomonas aeruginosa"</span>),
<span class="kw">VAN</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
<span class="kw">AMX</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
<span class="kw">COL</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span>
<span class="kw">CAZ</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
<span class="kw">CXM</span> <span class="kw">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
<span class="kw">PEN</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Penicillin G</span>
<span class="kw">FOX</span> <span class="kw">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">data</span></pre></body></html></div>
VAN = <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
AMX = <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
COL = <span class="st">"-"</span>, <span class="co"># Colistin</span>
CAZ = <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
CXM = <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
PEN = <span class="st">"S"</span>, <span class="co"># Penicillin G</span>
FOX = <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
stringsAsFactors = <span class="fl">FALSE</span>)
</pre></div>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="kw">data</span>
</pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
@@ -300,7 +306,9 @@
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>)</pre></body></html></div>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">data</span>)
</pre></div>
<pre><code># Warning: Not all columns with antimicrobial results are of class &lt;rsi&gt;.
# Transform eligible columns to class &lt;rsi&gt; on beforehand: your_data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></pre>
<table class="table">
@@ -385,7 +393,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

142
docs/articles/MDR.html
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@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -186,7 +186,7 @@
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
@@ -234,16 +234,20 @@
<a href="#examples" class="anchor"></a>Examples</h4>
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <span class="co"># to support pipes: %&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">cleaner</span>) <span class="co"># to create frequency tables</span></pre></body></html></div>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>() <span class="kw">%&gt;%</span>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>) <span class="co"># to support pipes: %&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://github.com/msberends/cleaner">cleaner</a></span>) <span class="co"># to create frequency tables</span>
</pre></div>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>() <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>() <span class="co"># show frequency table of the result</span>
<span class="co"># NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
<span class="co"># NOTE: Reliability would be improved if these antimicrobial results would be available too: ceftaroline (CPT), fusidic acid (FUS), telavancin (TLV), daptomycin (DAP), quinupristin/dalfopristin (QDA), minocycline (MNO), gentamicin-high (GEH), streptomycin-high (STH), doripenem (DOR), levofloxacin (LVX), netilmicin (NET), ticarcillin/clavulanic acid (TCC), ertapenem (ETP), cefotetan (CTT), aztreonam (ATM), ampicillin/sulbactam (SAM), polymyxin B (PLB)</span>
<span class="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span>
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></pre></body></html></div>
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 2,000<br>
@@ -279,55 +283,67 @@ Unique: 2</p>
</tbody>
</table>
<p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># a helper function to get a random vector with values S, I and R</span>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="co"># a helper function to get a random vector with values S, I and R</span>
<span class="co"># with the probabilities 50% - 10% - 40%</span>
<span class="no">sample_rsi</span> <span class="kw">&lt;-</span> <span class="kw">function</span>() {
<span class="kw">sample_rsi</span> <span class="op">&lt;-</span> <span class="fu">function</span>() {
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),
<span class="kw">size</span> <span class="kw">=</span> <span class="fl">5000</span>,
<span class="kw">prob</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),
<span class="kw">replace</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
size = <span class="fl">5000</span>,
prob = <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),
replace = <span class="fl">TRUE</span>)
}
<span class="no">my_TB_data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">rifampicin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">isoniazid</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">gatifloxacin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">ethambutol</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">pyrazinamide</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">moxifloxacin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">kanamycin</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>())</pre></body></html></div>
<span class="kw">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(rifampicin = <span class="fu">sample_rsi</span>(),
isoniazid = <span class="fu">sample_rsi</span>(),
gatifloxacin = <span class="fu">sample_rsi</span>(),
ethambutol = <span class="fu">sample_rsi</span>(),
pyrazinamide = <span class="fu">sample_rsi</span>(),
moxifloxacin = <span class="fu">sample_rsi</span>(),
kanamycin = <span class="fu">sample_rsi</span>())
</pre></div>
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">my_TB_data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">RIF</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">INH</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">GAT</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">ETH</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">PZA</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">MFX</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>(),
<span class="kw">KAN</span> <span class="kw">=</span> <span class="fu">sample_rsi</span>())</pre></body></html></div>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="kw">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(RIF = <span class="fu">sample_rsi</span>(),
INH = <span class="fu">sample_rsi</span>(),
GAT = <span class="fu">sample_rsi</span>(),
ETH = <span class="fu">sample_rsi</span>(),
PZA = <span class="fu">sample_rsi</span>(),
MFX = <span class="fu">sample_rsi</span>(),
KAN = <span class="fu">sample_rsi</span>())
</pre></div>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S S R R S I</span>
<span class="co"># 2 R S R R R S</span>
<span class="co"># 3 R S S S I S</span>
<span class="co"># 4 S S I S R S</span>
<span class="co"># 5 R I R S R S</span>
<span class="co"># 6 S S S S R R</span>
<span class="co"># 1 R R R R I I</span>
<span class="co"># 2 S S S R S R</span>
<span class="co"># 3 S I S S S S</span>
<span class="co"># 4 S I S R R R</span>
<span class="co"># 5 S S R S S R</span>
<span class="co"># 6 S R S R R R</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 I</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 S</span>
<span class="co"># 4 R</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span></pre></body></html></div>
<span class="co"># 4 S</span>
<span class="co"># 5 S</span>
<span class="co"># 6 R</span>
</pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="no">my_TB_data</span>, <span class="kw">guideline</span> <span class="kw">=</span> <span class="st">"TB"</span>)</pre></body></html></div>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="kw">my_TB_data</span>, guideline = <span class="st">"TB"</span>)
</pre></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">my_TB_data</span>$<span class="no">mdr</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span>(<span class="no">my_TB_data</span>)
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="kw">my_TB_data</span><span class="op">$</span><span class="kw">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span>
<span class="co"># NOTE: Auto-guessing columns suitable for analysis...OK.</span>
<span class="co"># NOTE: Reliability would be improved if these antimicrobial results would be available too: capreomycin (CAP), rifabutin (RIB), rifapentine (RFP)</span></pre></body></html></div>
<span class="co"># NOTE: Reliability would be improved if these antimicrobial results would be available too: capreomycin (CAP), rifabutin (RIB), rifapentine (RFP)</span>
</pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">my_TB_data</span>$<span class="no">mdr</span>)</pre></body></html></div>
<div class="sourceCode" id="cb8"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_TB_data</span><span class="op">$</span><span class="kw">mdr</span>)
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000<br>
@@ -347,40 +363,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3215</td>
<td align="right">64.30%</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">643</td>
<td align="right">12.86%</td>
<td align="right">3858</td>
<td align="right">77.16%</td>
<td align="left">Negative</td>
<td align="right">674</td>
<td align="right">13.48%</td>
<td align="right">3903</td>
<td align="right">78.06%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Negative</td>
<td align="right">637</td>
<td align="right">12.74%</td>
<td align="right">4495</td>
<td align="right">89.90%</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">616</td>
<td align="right">12.32%</td>
<td align="right">4519</td>
<td align="right">90.38%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">292</td>
<td align="right">5.84%</td>
<td align="right">4787</td>
<td align="right">95.74%</td>
<td align="right">285</td>
<td align="right">5.70%</td>
<td align="right">4804</td>
<td align="right">96.08%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">213</td>
<td align="right">4.26%</td>
<td align="right">196</td>
<td align="right">3.92%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
@@ -402,7 +418,7 @@ Unique: 5</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

60
docs/articles/PCA.html
View File

@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
<div class="hidden name"><code>PCA.Rmd</code></div>
@@ -204,9 +204,10 @@
<h1 class="hasAnchor">
<a href="#transforming" class="anchor"></a>Transforming</h1>
<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/reexports.html">glimpse</a></span>(<span class="no">example_isolates</span>)
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="fu"><a href="https://tibble.tidyverse.org/reference/glimpse.html">glimpse</a></span>(<span class="kw">example_isolates</span>)
<span class="co"># Rows: 2,000</span>
<span class="co"># Columns: 49</span>
<span class="co"># $ date &lt;date&gt; 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…</span>
@@ -257,16 +258,18 @@
<span class="co"># $ CHL &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ COL &lt;ord&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
<span class="co"># $ MUP &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ RIF &lt;ord&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></pre></body></html></div>
<span class="co"># $ RIF &lt;ord&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
</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"><html><body><pre class="r"><span class="no">resistance_data</span> <span class="kw">&lt;-</span> <span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">order</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">mo</span>), <span class="co"># group on anything, like order</span>
<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span> <span class="co"># and genus as we do here</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span>(<span class="no">is.rsi</span>, <span class="no">resistance</span>) <span class="kw">%&gt;%</span> <span class="co"># then get resistance of all drugs</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">order</span>, <span class="no">genus</span>, <span class="no">AMC</span>, <span class="no">CXM</span>, <span class="no">CTX</span>,
<span class="no">CAZ</span>, <span class="no">GEN</span>, <span class="no">TOB</span>, <span class="no">TMP</span>, <span class="no">SXT</span>) <span class="co"># and select only relevant columns</span>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="kw">resistance_data</span> <span class="op">&lt;-</span> <span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(order = <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="kw">mo</span>), <span class="co"># group on anything, like order</span>
genus = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span> <span class="co"># and genus as we do here</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span>(<span class="kw">is.rsi</span>, <span class="kw">resistance</span>) <span class="op">%&gt;%</span> <span class="co"># then get resistance of all drugs</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">order</span>, <span class="kw">genus</span>, <span class="kw">AMC</span>, <span class="kw">CXM</span>, <span class="kw">CTX</span>,
<span class="kw">CAZ</span>, <span class="kw">GEN</span>, <span class="kw">TOB</span>, <span class="kw">TMP</span>, <span class="kw">SXT</span>) <span class="co"># and select only relevant columns</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">resistance_data</span>)
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">resistance_data</span>)
<span class="co"># # A tibble: 6 x 10</span>
<span class="co"># # Groups: order [2]</span>
<span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span>
@@ -276,35 +279,46 @@
<span class="co"># 3 Actinomycetales Cutibacterium NA NA NA NA NA NA NA NA</span>
<span class="co"># 4 Actinomycetales Dermabacter NA NA NA NA NA NA NA NA</span>
<span class="co"># 5 Actinomycetales Micrococcus NA NA NA NA NA NA NA NA</span>
<span class="co"># 6 Actinomycetales Rothia NA NA NA NA NA NA NA NA</span></pre></body></html></div>
<span class="co"># 6 Actinomycetales Rothia NA NA NA NA NA NA NA NA</span>
</pre></div>
</div>
<div id="perform-principal-component-analysis" class="section level1">
<h1 class="hasAnchor">
<a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">pca_result</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span>(<span class="no">resistance_data</span>)
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="kw">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span>(<span class="kw">resistance_data</span>)
<span class="co"># NOTE: Columns selected for PCA: AMC CXM CTX CAZ GEN TOB TMP SXT.</span>
<span class="co"># Total observations available: 7.</span></pre></body></html></div>
<span class="co"># Total observations available: 7.</span>
</pre></div>
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">pca_result</span>)
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="kw">pca_result</span>)
<span class="co"># Importance of components:</span>
<span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span>
<span class="co"># Standard deviation 2.154 1.6809 0.61305 0.33882 0.20755 0.03137 1.602e-16</span>
<span class="co"># Proportion of Variance 0.580 0.3532 0.04698 0.01435 0.00538 0.00012 0.000e+00</span>
<span class="co"># Cumulative Proportion 0.580 0.9332 0.98014 0.99449 0.99988 1.00000 1.000e+00</span></pre></body></html></div>
<span class="co"># Cumulative Proportion 0.580 0.9332 0.98014 0.99449 0.99988 1.00000 1.000e+00</span>
</pre></div>
<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
</div>
<div id="plotting-the-results" class="section level1">
<h1 class="hasAnchor">
<a href="#plotting-the-results" class="anchor"></a>Plotting the results</h1>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span>(<span class="no">pca_result</span>)</pre></body></html></div>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span>(<span class="kw">pca_result</span>)
</pre></div>
<p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
<p>But we can’t see the explanation of the points. Perhaps this works better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>)</pre></body></html></div>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="kw">pca_result</span>)
</pre></div>
<p><img src="PCA_files/figure-html/unnamed-chunk-6-1.png" width="750"></p>
<p>You can also print an ellipse per group, and edit the appearance:</p>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>, <span class="kw">ellipse</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +
<span class="kw pkg">ggplot2</span><span class="kw ns">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="kw">title</span> <span class="kw">=</span> <span class="st">"An AMR/PCA biplot!"</span>)</pre></body></html></div>
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="kw">pca_result</span>, ellipse = <span class="fl">TRUE</span>) <span class="op">+</span>
<span class="kw">ggplot2</span>::<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(title = <span class="st">"An AMR/PCA biplot!"</span>)
</pre></div>
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
</div>
</div>
@@ -324,7 +338,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

84
docs/articles/SPSS.html
View File

@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -186,7 +186,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -240,7 +240,8 @@
</li>
</ul>
<p>To demonstrate the first point:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="co"># not all values are valid MIC values:</span>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="co"># not all values are valid MIC values:</span>
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 0.125</span>
@@ -253,13 +254,13 @@
<span class="co"># [1] "Gram-negative"</span>
<span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span>
<span class="no">klebsiella_test</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="st">"klebsiella"</span>,
<span class="kw">amox</span> <span class="kw">=</span> <span class="st">"S"</span>,
<span class="kw">stringsAsFactors</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="no">klebsiella_test</span> <span class="co"># (our original data)</span>
<span class="kw">klebsiella_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(mo = <span class="st">"klebsiella"</span>,
amox = <span class="st">"S"</span>,
stringsAsFactors = <span class="fl">FALSE</span>)
<span class="kw">klebsiella_test</span> <span class="co"># (our original data)</span>
<span class="co"># mo amox</span>
<span class="co"># 1 klebsiella S</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">klebsiella_test</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">klebsiella_test</span>, info = <span class="fl">FALSE</span>) <span class="co"># (the edited data by EUCAST rules)</span>
<span class="co"># mo amox</span>
<span class="co"># 1 klebsiella R</span>
@@ -271,7 +272,8 @@
<span class="co"># [4] "fluclox" "flucloxacilina" "flucloxacillin" </span>
<span class="co"># [7] "flucloxacilline" "flucloxacillinum" "fluorochloroxacillin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)
<span class="co"># [1] "J01CF05"</span></pre></body></html></div>
<span class="co"># [1] "J01CF05"</span>
</pre></div>
</div>
<div id="import-data-from-spsssasstata" class="section level2">
<h2 class="hasAnchor">
@@ -287,7 +289,8 @@
<p><img src="https://github.com/msberends/AMR/raw/master/docs/import2.png"></p>
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
<p>The difference is this:</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">SPSS_data</span>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="kw">SPSS_data</span>
<span class="co"># # A tibble: 4,203 x 4</span>
<span class="co"># v001 sex status statusage</span>
<span class="co"># &lt;dbl&gt; &lt;dbl+lbl&gt; &lt;dbl+lbl&gt; &lt;dbl&gt;</span>
@@ -303,7 +306,7 @@
<span class="co"># 10 10018 0 1 66.6</span>
<span class="co"># # … with 4,193 more rows</span>
<span class="fu">as_factor</span>(<span class="no">SPSS_data</span>)
<span class="fu">as_factor</span>(<span class="kw">SPSS_data</span>)
<span class="co"># # A tibble: 4,203 x 4</span>
<span class="co"># v001 sex status statusage</span>
<span class="co"># &lt;dbl&gt; &lt;fct&gt; &lt;fct&gt; &lt;dbl&gt;</span>
@@ -317,67 +320,82 @@
<span class="co"># 8 10011 Male alive 73.1</span>
<span class="co"># 9 10017 Male alive 56.7</span>
<span class="co"># 10 10018 Female alive 66.6</span>
<span class="co"># # … with 4,193 more rows</span></pre></body></html></div>
<span class="co"># # … with 4,193 more rows</span>
</pre></div>
</div>
<div id="base-r" class="section level3">
<h3 class="hasAnchor">
<a href="#base-r" class="anchor"></a>Base R</h3>
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/">great <code>haven</code> package</a> yourself:</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># download and install the latest version:</span>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="co"># download and install the latest version:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"haven"</span>)
<span class="co"># load the package you just installed:</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">haven</span>)</pre></body></html></div>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="http://haven.tidyverse.org">haven</a></span>)
</pre></div>
<p>You can now import files as follows:</p>
<div id="spss" class="section level4">
<h4 class="hasAnchor">
<a href="#spss" class="anchor"></a>SPSS</h4>
<p>To read files from SPSS into R:</p>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># read any SPSS file based on file extension (best way):</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="co"># read any SPSS file based on file extension (best way):</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span>(file = <span class="st">"path/to/file"</span>)
<span class="co"># read .sav or .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span>(file = <span class="st">"path/to/file"</span>)
<span class="co"># read .por file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span>(file = <span class="st">"path/to/file"</span>)
</pre></div>
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>, as mentioned above.</p>
<p>To export your R objects to the SPSS file format:</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="co"># save as .sav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="co"># save as .sav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</span>)
<span class="co"># save as compressed .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">compress</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</span>, compress = <span class="fl">TRUE</span>)
</pre></div>
</div>
<div id="sas" class="section level4">
<h4 class="hasAnchor">
<a href="#sas" class="anchor"></a>SAS</h4>
<p>To read files from SAS into R:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(<span class="kw">data_file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">catalog_file</span> <span class="kw">=</span> <span class="kw">NULL</span>)
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="co"># read .sas7bdat + .sas7bcat files:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span>(data_file = <span class="st">"path/to/file"</span>, catalog_file = <span class="kw">NULL</span>)
<span class="co"># read SAS transport files (version 5 and version 8):</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span>(file = <span class="st">"path/to/file"</span>)
</pre></div>
<p>To export your R objects to the SAS file format:</p>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="co"># save as regular SAS file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>)
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="co"># save as regular SAS file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</span>)
<span class="co"># the SAS transport format is an open format </span>
<span class="co"># (required for submission of the data to the FDA)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">8</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"path/to/file"</span>, version = <span class="fl">8</span>)
</pre></div>
</div>
<div id="stata" class="section level4">
<h4 class="hasAnchor">
<a href="#stata" class="anchor"></a>Stata</h4>
<p>To read files from Stata into R:</p>
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="co"># read .dta file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)
<div class="sourceCode" id="cb8"><pre class="downlit">
<span class="co"># read .dta file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span>(file = <span class="st">"/path/to/file"</span>)
<span class="co"># works exactly the same:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(<span class="kw">file</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span>(file = <span class="st">"/path/to/file"</span>)
</pre></div>
<p>To export your R objects to the Stata file format:</p>
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="co"># save as .dta file, Stata version 14:</span>
<div class="sourceCode" id="cb9"><pre class="downlit">
<span class="co"># save as .dta file, Stata version 14:</span>
<span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(<span class="kw">data</span> <span class="kw">=</span> <span class="no">yourdata</span>, <span class="kw">path</span> <span class="kw">=</span> <span class="st">"/path/to/file"</span>, <span class="kw">version</span> <span class="kw">=</span> <span class="fl">14</span>)</pre></body></html></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span>(data = <span class="kw">yourdata</span>, path = <span class="st">"/path/to/file"</span>, version = <span class="fl">14</span>)
</pre></div>
</div>
</div>
</div>
@@ -398,7 +416,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

54
docs/articles/WHONET.html
View File

@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -186,7 +186,7 @@
<h1 data-toc-skip>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@@ -200,34 +200,42 @@
<a href="#import-of-data" class="anchor"></a>Import of data</h3>
<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
<p>An example syntax could look like this:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">readxl</span>)
<span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/your/file.xlsx"</span>)</pre></body></html></div>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://readxl.tidyverse.org">readxl</a></span>)
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(path = <span class="st">"path/to/your/file.xlsx"</span>)
</pre></div>
<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
</div>
<div id="preparation" class="section level3">
<h3 class="hasAnchor">
<a href="#preparation" class="anchor"></a>Preparation</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="uri">https://www.tidyverse.org/</a>.</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <span class="co"># part of tidyverse</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">ggplot2</span>) <span class="co"># part of tidyverse</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>) <span class="co"># this package</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">cleaner</span>) <span class="co"># to create frequency tables</span></pre></body></html></div>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>) <span class="co"># part of tidyverse</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="http://ggplot2.tidyverse.org">ggplot2</a></span>) <span class="co"># part of tidyverse</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>) <span class="co"># this package</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://github.com/msberends/cleaner">cleaner</a></span>) <span class="co"># to create frequency tables</span>
</pre></div>
<p>We will have to transform some variables to simplify and automate the analysis:</p>
<ul>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
</ul>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># transform variables</span>
<span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">WHONET</span> <span class="kw">%&gt;%</span>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="co"># transform variables</span>
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="kw">WHONET</span> <span class="op">%&gt;%</span>
<span class="co"># get microbial ID based on given organism</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">mo</span> <span class="kw">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">Organism</span>)) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(mo = <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">Organism</span>)) <span class="op">%&gt;%</span>
<span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">AMP_ND10</span>:<span class="no">CIP_EE</span>), <span class="no">as.rsi</span>)</pre></body></html></div>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">AMP_ND10</span><span class="op">:</span><span class="kw">CIP_EE</span>), <span class="kw">as.rsi</span>)
</pre></div>
<p>No errors or warnings, so all values are transformed succesfully.</p>
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. Its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function can be used to create frequency tables.</p>
<p>So let’s check our data, with a couple of frequency tables:</p>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
<span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>), <span class="kw">nmax</span> <span class="kw">=</span> <span class="fl">10</span>)</pre></body></html></div>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
<span class="kw">data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">mo</span>), nmax = <span class="fl">10</span>)
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 500<br>
@@ -328,9 +336,11 @@ Longest: 40</p>
</tbody>
</table>
<p>(omitted 27 entries, n = 56 [11.20%])</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="co"># our transformed antibiotic columns</span>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="co"># our transformed antibiotic columns</span>
<span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
<span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">AMC_ND2</span>)</pre></body></html></div>
<span class="kw">data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">AMC_ND2</span>)
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 500<br>
@@ -378,10 +388,12 @@ Unique: 3</p>
<h3 class="hasAnchor">
<a href="#a-first-glimpse-at-results" class="anchor"></a>A first glimpse at results</h3>
<p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">Country</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">Country</span>, <span class="no">AMP_ND2</span>, <span class="no">AMC_ED20</span>, <span class="no">CAZ_ED10</span>, <span class="no">CIP_ED5</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span>(<span class="kw">translate_ab</span> <span class="kw">=</span> <span class="st">'ab'</span>, <span class="kw">facet</span> <span class="kw">=</span> <span class="st">"Country"</span>, <span class="kw">datalabels</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">Country</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">Country</span>, <span class="kw">AMP_ND2</span>, <span class="kw">AMC_ED20</span>, <span class="kw">CAZ_ED10</span>, <span class="kw">CIP_ED5</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span>(translate_ab = <span class="st">'ab'</span>, facet = <span class="st">"Country"</span>, datalabels = <span class="fl">FALSE</span>)
</pre></div>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
</div>
</div>
@@ -399,7 +411,7 @@ Unique: 3</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

202
docs/articles/benchmarks.html
View File

@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -197,13 +197,16 @@
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code>microbenchmark()</code> runs different input expressions independently of each other and measures their time-to-result.</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">microbenchmark</span> <span class="kw">&lt;-</span> <span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="no"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)</pre></body></html></div>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="kw">microbenchmark</span> <span class="op">&lt;-</span> <span class="kw">microbenchmark</span>::<span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
</pre></div>
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
<p>But the calculation time differs a lot:</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">S.aureus</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="kw">S.aureus</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),
@@ -218,47 +221,50 @@
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fl">22242419</span>), <span class="co"># Catalogue of Life ID</span>
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">2</span>)
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">2</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 11 12 17 13 15 51 10</span>
<span class="co"># as.mo("stau") 150 160 170 170 190 200 10</span>
<span class="co"># as.mo("STAU") 160 160 180 190 190 210 10</span>
<span class="co"># as.mo("staaur") 12 13 23 15 20 68 10</span>
<span class="co"># as.mo("STAAUR") 11 12 20 16 18 44 10</span>
<span class="co"># as.mo("S. aureus") 11 13 29 17 44 84 10</span>
<span class="co"># as.mo("S aureus") 11 15 21 16 18 46 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 11 13 16 13 15 41 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870 890 920 900 950 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 400 410 430 440 450 490 10</span>
<span class="co"># as.mo("MRSA") 13 13 17 14 16 40 10</span>
<span class="co"># as.mo("VISA") 14 17 25 19 36 46 10</span>
<span class="co"># as.mo("VRSA") 13 15 21 17 21 50 10</span>
<span class="co"># as.mo(22242419) 130 140 150 150 150 180 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 11.0 14 21 15 16 51 10</span>
<span class="co"># as.mo("stau") 170.0 170 190 190 210 240 10</span>
<span class="co"># as.mo("STAU") 160.0 170 180 180 200 210 10</span>
<span class="co"># as.mo("staaur") 11.0 13 19 14 18 48 10</span>
<span class="co"># as.mo("STAAUR") 11.0 13 22 17 37 40 10</span>
<span class="co"># as.mo("S. aureus") 15.0 15 24 17 26 56 10</span>
<span class="co"># as.mo("S aureus") 12.0 13 21 16 23 49 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 9.8 13 21 14 15 65 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 960.0 960 1100 980 1100 1400 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 440.0 450 480 470 480 570 10</span>
<span class="co"># as.mo("MRSA") 12.0 14 22 15 17 86 10</span>
<span class="co"># as.mo("VISA") 15.0 18 25 19 40 42 10</span>
<span class="co"># as.mo("VRSA") 14.0 15 30 22 44 69 10</span>
<span class="co"># as.mo(22242419) 130.0 150 160 170 180 190 10</span>
</pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">M.semesiae</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="kw">M.semesiae</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Methanosarcina semesiae"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">M.semesiae</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 176.800 179.200 189.20 185.90 194.00 212.60</span>
<span class="co"># as.mo("METSEM") 164.400 170.800 193.00 188.20 211.10 243.00</span>
<span class="co"># as.mo("M. semesiae") 10.950 11.310 19.92 15.41 18.79 50.84</span>
<span class="co"># as.mo("M. semesiae") 11.560 11.860 17.66 14.15 16.96 50.76</span>
<span class="co"># as.mo("Methanosarcina semesiae") 9.408 9.669 18.03 14.12 15.24 42.57</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 186.900 192.90 204.70 199.10 207.70 251.20</span>
<span class="co"># as.mo("METSEM") 175.500 199.70 215.20 218.20 232.00 240.40</span>
<span class="co"># as.mo("M. semesiae") 11.500 13.29 16.47 13.85 16.84 36.90</span>
<span class="co"># as.mo("M. semesiae") 11.690 11.94 16.81 14.40 15.75 42.76</span>
<span class="co"># as.mo("Methanosarcina semesiae") 9.688 10.28 14.55 11.99 13.72 39.41</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span></pre></body></html></div>
<span class="co"># 10</span>
</pre></div>
<p>Looking up arbitrary codes of less prevalent microorganisms costs the most time. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></p>
@@ -267,102 +273,110 @@
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># take all MO codes from the example_isolates data set</span>
<span class="no">x</span> <span class="kw">&lt;-</span> <span class="no">example_isolates</span>$<span class="no">mo</span> <span class="kw">%&gt;%</span>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="co"># take all MO codes from the example_isolates data set</span>
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="kw">example_isolates</span><span class="op">$</span><span class="kw">mo</span> <span class="op">%&gt;%</span>
<span class="co"># keep only the unique ones</span>
<span class="fu"><a href="https://rdrr.io/r/base/unique.html">unique</a></span>() <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/base/unique.html">unique</a></span>() <span class="op">%&gt;%</span>
<span class="co"># pick 50 of them at random</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fl">50</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fl">50</span>) <span class="op">%&gt;%</span>
<span class="co"># paste that 10,000 times</span>
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">10000</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">10000</span>) <span class="op">%&gt;%</span>
<span class="co"># scramble it</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>()
<span class="co"># got indeed 50 times 10,000 = half a million?</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span>(<span class="no">x</span>)
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span>(<span class="kw">x</span>)
<span class="co"># [1] 500000</span>
<span class="co"># and how many unique values do we have?</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(<span class="no">x</span>)
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(<span class="kw">x</span>)
<span class="co"># [1] 50</span>
<span class="co"># now let's see:</span>
<span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">x</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">x</span>),
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 1720 1760 1820 1800 1830 1990 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.8 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 1840 1870 1950 1940 1980 2140 10</span>
</pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.94 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
C = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.16 8.35 9.06 8.97 9.75 10.20 10</span>
<span class="co"># B 10.50 10.60 15.50 12.20 12.80 49.90 10</span>
<span class="co"># C 1.04 1.15 1.21 1.19 1.27 1.53 10</span></pre></body></html></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0012 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
<span class="kw">D</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),
<span class="kw">E</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),
<span class="kw">F</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),
<span class="kw">G</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),
<span class="kw">H</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># A 8.17 8.49 9.32 9.32 9.90 10.90 10</span>
<span class="co"># B 10.90 11.80 16.30 13.20 14.70 45.60 10</span>
<span class="co"># C 1.06 1.22 1.32 1.28 1.44 1.57 10</span>
</pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0013 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
C = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
D = <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),
E = <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),
F = <span class="fu"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),
G = <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),
H = <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.948 0.971 1.14 1.020 1.39 1.52 10</span>
<span class="co"># B 0.968 1.040 1.22 1.190 1.41 1.56 10</span>
<span class="co"># C 0.979 1.020 1.31 1.260 1.58 1.66 10</span>
<span class="co"># D 0.964 1.010 1.24 1.190 1.45 1.83 10</span>
<span class="co"># E 0.977 0.995 1.15 1.030 1.40 1.45 10</span>
<span class="co"># F 0.878 0.982 1.11 1.010 1.37 1.43 10</span>
<span class="co"># G 0.929 0.961 1.18 1.000 1.43 1.58 10</span>
<span class="co"># H 0.901 0.967 1.09 0.998 1.35 1.40 10</span></pre></body></html></div>
<span class="co"># A 1.020 1.030 1.11 1.060 1.22 1.33 10</span>
<span class="co"># B 0.982 1.010 1.10 1.040 1.21 1.38 10</span>
<span class="co"># C 0.992 1.020 1.13 1.040 1.24 1.58 10</span>
<span class="co"># D 0.987 1.000 1.07 1.030 1.08 1.29 10</span>
<span class="co"># E 0.978 0.982 1.02 0.999 1.03 1.15 10</span>
<span class="co"># F 0.975 0.992 1.05 1.000 1.03 1.26 10</span>
<span class="co"># G 0.976 0.983 1.02 0.994 1.03 1.22 10</span>
<span class="co"># H 0.977 1.010 1.11 1.090 1.21 1.28 10</span>
</pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
<h3 class="hasAnchor">
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span>
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span>
<span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
<span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
<span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span>
<span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="kw">en</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>),
<span class="kw">de</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>),
<span class="kw">nl</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>),
<span class="kw">es</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>),
<span class="kw">it</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"it"</span>),
<span class="kw">fr</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"fr"</span>),
<span class="kw">pt</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>),
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(en = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"en"</span>),
de = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"de"</span>),
nl = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"nl"</span>),
es = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"es"</span>),
it = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"it"</span>),
fr = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"fr"</span>),
pt = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"pt"</span>),
times = <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 12.09 12.46 15.90 13.86 14.55 57.62 100</span>
<span class="co"># de 12.92 13.26 19.73 14.63 16.01 61.55 100</span>
<span class="co"># nl 16.53 17.00 20.26 17.64 19.93 57.54 100</span>
<span class="co"># es 12.98 13.28 18.27 14.76 15.64 179.30 100</span>
<span class="co"># it 12.92 13.15 19.20 14.08 16.08 64.07 100</span>
<span class="co"># fr 12.99 13.21 17.81 13.59 15.71 67.97 100</span>
<span class="co"># pt 13.00 13.23 17.30 14.35 15.65 69.85 100</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 12.40 14.34 17.88 14.89 15.48 55.22 100</span>
<span class="co"># de 13.17 14.30 17.90 15.84 16.66 56.60 100</span>
<span class="co"># nl 17.14 19.86 24.99 20.78 21.70 64.66 100</span>
<span class="co"># es 13.43 15.29 17.65 15.93 16.59 54.38 100</span>
<span class="co"># it 13.33 14.83 18.35 15.68 16.36 57.61 100</span>
<span class="co"># fr 13.40 15.43 18.66 16.01 16.59 54.35 100</span>
<span class="co"># pt 13.47 15.33 18.93 16.15 16.84 57.28 100</span>
</pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>
@@ -380,7 +394,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -263,7 +263,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

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@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -186,7 +186,7 @@
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 July 2020</h4>
<h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd"><code>vignettes/resistance_predict.Rmd</code></a></small>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
@@ -200,35 +200,38 @@
<a href="#needed-r-packages" class="anchor"></a>Needed R packages</h2>
<p>As with many uses in R, we need some additional packages for AMR analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">ggplot2</span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="http://ggplot2.tidyverse.org">ggplot2</a></span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
<span class="co"># (if not yet installed, install with:)</span>
<span class="co"># install.packages(c("tidyverse", "AMR"))</span></pre></body></html></div>
<span class="co"># install.packages(c("tidyverse", "AMR"))</span>
</pre></div>
</div>
<div id="prediction-analysis" class="section level2">
<h2 class="hasAnchor">
<a href="#prediction-analysis" class="anchor"></a>Prediction analysis</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 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"><html><body><pre class="r"># resistance prediction of piperacillin/tazobactam (TZP):
resistance_predict(tbl = example_isolates, col_date = "date", col_ab = "TZP", model = "binomial")
# or:
example_isolates %&gt;%
resistance_predict(col_ab = "TZP",
model "binomial")
# to bind it to object 'predict_TZP' for example:
predict_TZP &lt;- example_isolates %&gt;%
resistance_predict(col_ab = "TZP",
model = "binomial")</pre></body></html></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
<span id="cb2-2"><a href="#cb2-2"></a><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
<span id="cb2-3"><a href="#cb2-3"></a></span>
<span id="cb2-4"><a href="#cb2-4"></a><span class="co"># or:</span></span>
<span id="cb2-5"><a href="#cb2-5"></a>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-6"><a href="#cb2-6"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
<span id="cb2-7"><a href="#cb2-7"></a> model <span class="st">"binomial"</span>)</span>
<span id="cb2-8"><a href="#cb2-8"></a></span>
<span id="cb2-9"><a href="#cb2-9"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
<span id="cb2-10"><a href="#cb2-10"></a>predict_TZP &lt;-<span class="st"> </span>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-11"><a href="#cb2-11"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
<span id="cb2-12"><a href="#cb2-12"></a> <span class="dt">model =</span> <span class="st">"binomial"</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><a href="../reference/resistance_predict.html">resistance_predict(..., info = FALSE)</a></code>.</p>
<pre><code># NOTE: Using column `date` as input for `col_date`.</code></pre>
<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="cb4"><html><body><pre class="r"><span class="no">predict_TZP</span>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="kw">predict_TZP</span>
<span class="co"># year value se_min se_max observations observed estimated</span>
<span class="co"># 1 2002 0.20000000 NA NA 15 0.20000000 0.05616378</span>
<span class="co"># 2 2003 0.06250000 NA NA 32 0.06250000 0.06163839</span>
@@ -258,27 +261,36 @@ predict_TZP &lt;- example_isolates %&gt;%
<span class="co"># 26 2027 0.41315710 0.3244399 0.5018743 NA NA 0.41315710</span>
<span class="co"># 27 2028 0.43730688 0.3418075 0.5328063 NA NA 0.43730688</span>
<span class="co"># 28 2029 0.46175755 0.3597639 0.5637512 NA NA 0.46175755</span>
<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span></pre></body></html></div>
<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span>
</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="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">predict_TZP</span>)</pre></body></html></div>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span>(<span class="kw">predict_TZP</span>)
</pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">predict_TZP</span>)</pre></body></html></div>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">predict_TZP</span>)
</pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<div class="sourceCode" id="cb7"><html><body><pre class="r">
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="co"># choose for error bars instead of a ribbon</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">predict_TZP</span>, <span class="kw">ribbon</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">predict_TZP</span>, ribbon = <span class="fl">FALSE</span>)
</pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
<div id="choosing-the-right-model" class="section level3">
<h3 class="hasAnchor">
<a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="no">mo</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="kw">==</span> <span class="st">"Gram-positive"</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"VAN"</span>, <span class="kw">year_min</span> <span class="kw">=</span> <span class="fl">2010</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"binomial"</span>) <span class="kw">%&gt;%</span>
<div class="sourceCode" id="cb8"><pre class="downlit">
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="kw">mo</span>, language = <span class="kw">NULL</span>) <span class="op">==</span> <span class="st">"Gram-positive"</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(col_ab = <span class="st">"VAN"</span>, year_min = <span class="fl">2010</span>, info = <span class="fl">FALSE</span>, model = <span class="st">"binomial"</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></body></html></div>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
</pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
@@ -319,25 +331,29 @@ predict_TZP &lt;- example_isolates %&gt;%
</tbody>
</table>
<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="no">mo</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="kw">==</span> <span class="st">"Gram-positive"</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"VAN"</span>, <span class="kw">year_min</span> <span class="kw">=</span> <span class="fl">2010</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">model</span> <span class="kw">=</span> <span class="st">"linear"</span>) <span class="kw">%&gt;%</span>
<div class="sourceCode" id="cb9"><pre class="downlit">
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="kw">mo</span>, language = <span class="kw">NULL</span>) <span class="op">==</span> <span class="st">"Gram-positive"</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(col_ab = <span class="st">"VAN"</span>, year_min = <span class="fl">2010</span>, info = <span class="fl">FALSE</span>, model = <span class="st">"linear"</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span></pre></body></html></div>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
</pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<p>This seems more likely, doesn’t it?</p>
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">model</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span>(<span class="no">predict_TZP</span>)$<span class="no">model</span>
<div class="sourceCode" id="cb10"><pre class="downlit">
<span class="kw">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span>(<span class="kw">predict_TZP</span>)<span class="op">$</span><span class="kw">model</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">model</span>)$<span class="no">family</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="kw">model</span>)<span class="op">$</span><span class="kw">family</span>
<span class="co"># </span>
<span class="co"># Family: binomial </span>
<span class="co"># Link function: logit</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">model</span>)$<span class="no">coefficients</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="kw">model</span>)<span class="op">$</span><span class="kw">coefficients</span>
<span class="co"># Estimate Std. Error z value Pr(&gt;|z|)</span>
<span class="co"># (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span>
<span class="co"># year 0.09883005 0.02295317 4.305725 1.664395e-05</span></pre></body></html></div>
<span class="co"># year 0.09883005 0.02295317 4.305725 1.664395e-05</span>
</pre></div>
</div>
</div>
</div>
@@ -357,7 +373,7 @@ predict_TZP &lt;- example_isolates %&gt;%
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

5
docs/articles/welcome_to_AMR.html
View File

@@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -195,6 +195,7 @@
<p><strong>READ ALL VIGNETTES <a href="https://msberends.github.io/AMR/articles/">ON OUR WEBSITE</a></strong></p>
<div id="welcome-to-the-amr-package" class="section level1">
<h1 class="hasAnchor">
<a href="#welcome-to-the-amr-package" class="anchor"></a>Welcome to the AMR package</h1>
@@ -243,7 +244,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/authors.html
View File

@@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -310,7 +310,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

16
docs/index.html
View File

@@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -192,7 +192,7 @@
</h1></div>
<blockquote>
<p><em>July 2020</em><br><span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> <strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br>
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! <br><a class="btn btn-info btn-amr">Take me to the 5-min survey!</a></p>
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! <br><a class="btn btn-info btn-amr" href="./survey.html">Take me to the 5-min survey!</a></p>
</blockquote>
<div id="what-is-amr-for-r" class="section level3">
<h3 class="hasAnchor">
@@ -246,7 +246,9 @@ Since you are one of our users, we would like to know how you use the package an
<h4 class="hasAnchor">
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)</pre></div>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)
</pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
@@ -254,8 +256,10 @@ Since you are one of our users, we would like to know how you use the package an
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p>The latest and unpublished development version can be installed from GitHub using:</p>
<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)
<span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span>(<span class="st">"msberends/AMR"</span>)</pre></div>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)
<span class="kw">remotes</span>::<span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span>(<span class="st">"msberends/AMR"</span>)
</pre></div>
</div>
</div>
<div id="get-started" class="section level3">
@@ -419,7 +423,7 @@ Since you are one of our users, we would like to know how you use the package an
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

400
docs/news/index.html
View File

@@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -229,9 +229,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309000" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9000">
<a href="#amr-1309000" class="anchor"></a>AMR 1.3.0.9000<small> Unreleased </small>
<div id="amr-1309001" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9001">
<a href="#amr-1309001" class="anchor"></a>AMR 1.3.0.9001<small> Unreleased </small>
</h1>
<div id="last-updated-10-august-2020" class="section level2">
<h2 class="hasAnchor">
@@ -243,13 +243,15 @@
<ul>
<li>
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.</p>
<div class="sourceCode" id="cb1"><pre class="r"><span class="co"># until dplyr 1.0.0</span>
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate_if</span>(<span class="no">is.mic</span>, <span class="no">as.rsi</span>)
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate_if</span>(<span class="no">is.disk</span>, <span class="no">as.rsi</span>)
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="co"># until dplyr 1.0.0</span>
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.mic</span>, <span class="kw">as.rsi</span>)
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.disk</span>, <span class="kw">as.rsi</span>)
<span class="co"># since dplyr 1.0.0</span>
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(<span class="no">is.mic</span>), <span class="no">as.rsi</span>))
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(<span class="no">is.disk</span>), <span class="no">as.rsi</span>))</pre></div>
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.mic</span>), <span class="kw">as.rsi</span>))
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.disk</span>), <span class="kw">as.rsi</span>))
</pre></div>
</li>
</ul>
</div>
@@ -266,12 +268,14 @@
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
<span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span>())
<span class="co">#&gt; Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span></pre></div>
<span class="co">#&gt; Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span>
</pre></div>
</li>
<li><p>Added <code><a href="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><a href="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
<li><p>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</p></li>
@@ -294,7 +298,7 @@
<ul>
<li>95% speed improvement by using other base R functions for calculation</li>
<li>Using unexisting columns wil now return an error instead of dropping them silently</li>
<li>Using variables for column names (as well as selectors like <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again</li>
<li>Using variables for column names (as well as selectors like <code><a href="https://tidyselect.r-lib.org/reference/all_of.html">dplyr::all_of()</a></code>) now works again</li>
</ul>
</li>
<li>
@@ -349,7 +353,7 @@
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p>
<ul>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://rdrr.io/pkg/cleaner/man">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
<li>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</li>
<li>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</li>
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@@ -453,11 +457,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb3"><pre class="r"><span class="no">yourdata</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="st">"E. coli"</span>)
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="kw">yourdata</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="st">"E. coli"</span>)
<span class="no">yourdata</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="no">.</span>$<span class="no">mybacteria</span>)</pre></div>
<span class="kw">yourdata</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="kw">.</span><span class="op">$</span><span class="kw">mybacteria</span>)
</pre></div>
</li>
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
@@ -480,21 +486,25 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
<div class="sourceCode" id="cb4"><pre class="r"><span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
<span class="co">#&gt; [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)
<span class="co">#&gt; [1] "Ampicillin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"21066-6"</span>)
<span class="co">#&gt; [1] "J01CA01"</span></pre></div>
<span class="co">#&gt; [1] "J01CA01"</span>
</pre></div>
</li>
<li>
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
<div class="sourceCode" id="cb5"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
<span class="co">#&gt; [1] 115329001 3092008 113961008</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>)
<span class="co">#&gt; [1] "Staphylococcus aureus"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="fl">115329001</span>)
<span class="co">#&gt; [1] "Gram-positive"</span></pre></div>
<span class="co">#&gt; [1] "Gram-positive"</span>
</pre></div>
</li>
</ul>
</li>
@@ -552,9 +562,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
<div class="sourceCode" id="cb6"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="no">...</span></pre></div>
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="kw">...</span>
</pre></div>
<p>then please adjust this to:</p>
<div class="sourceCode" id="cb7"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacterales"</span>) <span class="no">...</span></pre></div>
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacterales"</span>) <span class="kw">...</span>
</pre></div>
</li>
</ul>
</li>
@@ -566,12 +580,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
<div class="sourceCode" id="cb8"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">bug</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="kw">amoxicillin</span> <span class="kw">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>),
<span class="kw">amox_clav</span> <span class="kw">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMC</span>)) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(!<span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="no">amoxicillin</span>) <span class="kw">|</span> !<span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="no">amox_clav</span>))</pre></div>
<div class="sourceCode" id="cb8"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(bug = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(amoxicillin = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>),
amox_clav = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMC</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amoxicillin</span>) <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amox_clav</span>))
</pre></div>
</li>
<li>
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).</p>
@@ -593,7 +609,8 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
<li>
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
<div class="sourceCode" id="cb9"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
<div class="sourceCode" id="cb9"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
<span class="st">"staphylokok aureuz"</span>))
<span class="co">#&gt; Warning: </span>
<span class="co">#&gt; Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
@@ -602,7 +619,8 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span>()
<span class="co">#&gt; "Stafylococcus aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span>
<span class="co">#&gt; "staphylokok aureuz" -&gt; Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></pre></div>
<span class="co">#&gt; "staphylokok aureuz" -&gt; Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span>
</pre></div>
</li>
</ul>
</li>
@@ -650,25 +668,29 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
<div class="sourceCode" id="cb10"><pre class="r"><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">...</span>, <span class="kw">include_unknown</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></div>
<div class="sourceCode" id="cb10"><pre class="downlit">
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">...</span>, include_unknown = <span class="fl">TRUE</span>)
</pre></div>
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
</li>
<li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
<div class="sourceCode" id="cb11"><pre class="r"><span class="co"># how it works in base R:</span>
<span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
<span class="no">x</span>[<span class="fl">1</span>] <span class="kw">&lt;-</span> <span class="st">"B"</span>
<div class="sourceCode" id="cb11"><pre class="downlit">
<span class="co"># how it works in base R:</span>
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
<span class="kw">x</span>[<span class="fl">1</span>] <span class="op">&lt;-</span> <span class="st">"B"</span>
<span class="co">#&gt; Warning message:</span>
<span class="co">#&gt; invalid factor level, NA generated</span>
<span class="co"># how it now works similarly for classes 'mo' and 'ab':</span>
<span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
<span class="no">x</span>[<span class="fl">1</span>] <span class="kw">&lt;-</span> <span class="st">"testvalue"</span>
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
<span class="kw">x</span>[<span class="fl">1</span>] <span class="op">&lt;-</span> <span class="st">"testvalue"</span>
<span class="co">#&gt; Warning message:</span>
<span class="co">#&gt; invalid microorganism code, NA generated</span></pre></div>
<span class="co">#&gt; invalid microorganism code, NA generated</span>
</pre></div>
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
</li>
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
@@ -678,9 +700,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<div class="sourceCode" id="cb12"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>)
<div class="sourceCode" id="cb12"><pre class="downlit">
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>)
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="no">x</span>[<span class="fl">1</span>:<span class="fl">4</span>, ]
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, ]
<span class="co">#&gt; mo ab S I R total</span>
<span class="co">#&gt; 1 A. baumannii AMC 0 0 3 3</span>
<span class="co">#&gt; 2 A. baumannii AMK 0 0 0 0</span>
@@ -689,45 +712,52 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
<span class="co"># change the transformation with the FUN argument to anything you like:</span>
<span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>, <span class="kw">FUN</span> <span class="kw">=</span> <span class="no">mo_gramstain</span>)
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>, FUN = <span class="kw">mo_gramstain</span>)
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="no">x</span>[<span class="fl">1</span>:<span class="fl">4</span>, ]
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, ]
<span class="co">#&gt; mo ab S I R total</span>
<span class="co">#&gt; 1 Gram-negative AMC 469 89 174 732</span>
<span class="co">#&gt; 2 Gram-negative AMK 251 0 2 253</span>
<span class="co">#&gt; 3 Gram-negative AMP 227 0 405 632</span>
<span class="co">#&gt; 4 Gram-negative AMX 227 0 405 632</span>
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div>
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
</pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<div class="sourceCode" id="cb13"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="no">x</span>, <span class="kw">combine_IR</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></div>
<div class="sourceCode" id="cb13"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="kw">x</span>, combine_IR = <span class="fl">FALSE</span>)
</pre></div>
</li>
<li>
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
<div class="sourceCode" id="cb14"><pre class="r"># --------------------------------------------------------------------
# only_all_tested = FALSE only_all_tested = TRUE
# ----------------------- -----------------------
# Drug A Drug B include as include as include as include as
# numerator denominator numerator denominator
# -------- -------- ---------- ----------- ---------- -----------
# S or I S or I X X X X
# R S or I X X X X
# &lt;NA&gt; S or I X X - -
# S or I R X X X X
# R R - X - X
# &lt;NA&gt; R - - - -
# S or I &lt;NA&gt; X X - -
# R &lt;NA&gt; - - - -
# &lt;NA&gt; &lt;NA&gt; - - - -
# --------------------------------------------------------------------</pre></div>
<div class="sourceCode" id="cb14"><pre class="downlit">
<span class="co"># --------------------------------------------------------------------</span>
<span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span>
<span class="co"># ----------------------- -----------------------</span>
<span class="co"># Drug A Drug B include as include as include as include as</span>
<span class="co"># numerator denominator numerator denominator</span>
<span class="co"># -------- -------- ---------- ----------- ---------- -----------</span>
<span class="co"># S or I S or I X X X X</span>
<span class="co"># R S or I X X X X</span>
<span class="co"># &lt;NA&gt; S or I X X - -</span>
<span class="co"># S or I R X X X X</span>
<span class="co"># R R - X - X</span>
<span class="co"># &lt;NA&gt; R - - - -</span>
<span class="co"># S or I &lt;NA&gt; X X - -</span>
<span class="co"># R &lt;NA&gt; - - - -</span>
<span class="co"># &lt;NA&gt; &lt;NA&gt; - - - -</span>
<span class="co"># --------------------------------------------------------------------</span>
</pre></div>
<p>Since this is a major change, usage of the old <code>also_single_tested</code> will throw an informative error that it has been replaced by <code>only_all_tested</code>.</p>
</li>
<li>
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
<div class="sourceCode" id="cb15"><pre class="r"><span class="co"># (run this on your own console, as this page does not support colour printing)</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">mo</span>:<span class="no">AMC</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</pre></div>
<div class="sourceCode" id="cb15"><pre class="downlit">
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">mo</span><span class="op">:</span><span class="kw">AMC</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span>()
</pre></div>
</li>
</ul>
</div>
@@ -804,14 +834,16 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb16"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">AMX</span>, <span class="no">CIP</span>) <span class="kw">%&gt;%</span>
<div class="sourceCode" id="cb16"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">AMX</span>, <span class="kw">CIP</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>()
<span class="co"># antibiotic interpretation value isolates</span>
<span class="co"># 1 Amoxicillin SI 0.4442636 546</span>
<span class="co"># 2 Amoxicillin R 0.5557364 683</span>
<span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span>
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></pre></div>
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span>
</pre></div>
</li>
<li>
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
@@ -829,12 +861,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
</ul>
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb17"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
<div class="sourceCode" id="cb17"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
<span class="co"># B_ESCHR_COL</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
<span class="co"># "Escherichia coli"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)
<span class="co"># "Gram-negative"</span></pre></div>
<span class="co"># "Gram-negative"</span>
</pre></div>
</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
@@ -862,7 +896,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
<li>Small improvements to <code><a href="https://rdrr.io/r/base/plot.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> for MIC and RSI classes</li>
<li>Small improvements to <code><a href="https://rdrr.io/r/graphics/plot.default.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> for MIC and RSI classes</li>
<li>Allow Catalogue of Life IDs to be coerced by <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
</ul>
@@ -925,21 +959,23 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
</li>
<li>Frequency tables (<code>freq()</code>):
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
<ul>
<li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li>
<li><p>when all values are unique it now shows a message instead of a warning</p></li>
<li>
<p>support for boxplots:</p>
<div class="sourceCode" id="cb18"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">age</span>) <span class="kw">%&gt;%</span>
<div class="sourceCode" id="cb18"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
<span class="co"># grouped boxplots:</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">age</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</pre></div>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
</pre></div>
</li>
</ul>
</li>
@@ -948,7 +984,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@@ -1025,7 +1061,8 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<div class="sourceCode" id="cb19"><pre class="r"><span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
<div class="sourceCode" id="cb19"><pre class="downlit">
<span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()
@@ -1035,23 +1072,28 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</pre></div>
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()
</pre></div>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<div class="sourceCode" id="cb20"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>)
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>, <span class="kw">scope</span> <span class="kw">=</span> <span class="st">"all"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></pre></div>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>, scope = <span class="st">"all"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span>
</pre></div>
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb21"><pre class="r"><span class="no">ab_property</span> <span class="kw">-&gt;</span> <span class="fu">atc_property</span>()
<span class="no">ab_name</span> <span class="kw">-&gt;</span> <span class="fu">atc_name</span>()
<span class="no">ab_official</span> <span class="kw">-&gt;</span> <span class="fu">atc_official</span>()
<span class="no">ab_trivial_nl</span> <span class="kw">-&gt;</span> <span class="fu">atc_trivial_nl</span>()
<span class="no">ab_certe</span> <span class="kw">-&gt;</span> <span class="fu">atc_certe</span>()
<span class="no">ab_umcg</span> <span class="kw">-&gt;</span> <span class="fu">atc_umcg</span>()
<span class="no">ab_tradenames</span> <span class="kw">-&gt;</span> <span class="fu">atc_tradenames</span>()</pre></div>
<p>These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</p>
<div class="sourceCode" id="cb21"><pre class="downlit">
<span class="kw">ab_property</span> <span class="op">-&gt;</span> <span class="fu">atc_property</span>()
<span class="kw">ab_name</span> <span class="op">-&gt;</span> <span class="fu">atc_name</span>()
<span class="kw">ab_official</span> <span class="op">-&gt;</span> <span class="fu">atc_official</span>()
<span class="kw">ab_trivial_nl</span> <span class="op">-&gt;</span> <span class="fu">atc_trivial_nl</span>()
<span class="kw">ab_certe</span> <span class="op">-&gt;</span> <span class="fu">atc_certe</span>()
<span class="kw">ab_umcg</span> <span class="op">-&gt;</span> <span class="fu">atc_umcg</span>()
<span class="kw">ab_tradenames</span> <span class="op">-&gt;</span> <span class="fu">atc_tradenames</span>()
</pre></div>
<p>These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online_property.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</p>
</li>
<li><p>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</p></li>
<li><p>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</p></li>
@@ -1062,21 +1104,27 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age in years</p></li>
<li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</p></li>
<li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/base/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb22"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="no">septic_patients</span>, <span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"amox"</span>)
<span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">x</span>)
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">x</span>)</pre></div>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/graphics/plot.default.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb22"><pre class="downlit">
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">septic_patients</span>, col_ab = <span class="st">"amox"</span>)
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span>(<span class="kw">x</span>)
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">x</span>)
</pre></div>
</li>
<li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb23"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">...</span>)
<div class="sourceCode" id="cb23"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">...</span>)
<span class="co"># or</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)</pre></div>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)
</pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb24"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">only_firsts</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">only_firsts</span> <span class="kw">==</span> <span class="fl">TRUE</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">only_firsts</span>)</pre></div>
<div class="sourceCode" id="cb24"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(only_firsts = <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">only_firsts</span> <span class="op">==</span> <span class="fl">TRUE</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">only_firsts</span>)
</pre></div>
</li>
<li><p>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code></p></li>
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
@@ -1097,40 +1145,46 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Removed data sets <code>microorganisms.oldDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganismsDT</code> since they were no longer needed and only contained info already available in the <code>microorganisms</code> data set</li>
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
<li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
<li>Functions <code>atc_ddd()</code> and <code>atc_groups()</code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
<li>Functions <code>atc_ddd()</code> and <code>atc_groups()</code> have been renamed <code><a href="../reference/atc_online_property.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online_property.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
<li>Function <code>guess_mo()</code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Function <code>guess_atc()</code> is now deprecated in favour of <code>as.atc()</code> and will be removed in future versions</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<div class="sourceCode" id="cb25"><pre class="r"><span class="co"># mo_fullname() uses as.mo() internally</span>
<div class="sourceCode" id="cb25"><pre class="downlit">
<span class="co"># mo_fullname() uses as.mo() internally</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)
<span class="co">#&gt; [1] "Staphylococcus aureus"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)
<span class="co">#&gt; [1] "Staphylococcus kloosii"</span></pre></div>
<span class="co">#&gt; [1] "Staphylococcus kloosii"</span>
</pre></div>
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
<div class="sourceCode" id="cb26"><pre class="r"><span class="co"># equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">2</span>)
<div class="sourceCode" id="cb26"><pre class="downlit">
<span class="co"># equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">TRUE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">2</span>)
<span class="co"># also equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">0</span>)</pre></div>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">FALSE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">0</span>)
</pre></div>
<p>Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</p>
</li>
<li><p>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em></p></li>
<li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb27"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>)
<div class="sourceCode" id="cb27"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, language = <span class="st">"es"</span>)
<span class="co"># Warning: </span>
<span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
<span class="co">#&gt; [1] "(género desconocido)"</span></pre></div>
<span class="co">#&gt; [1] "(género desconocido)"</span>
</pre></div>
</li>
<li><p>Fix for vector containing only empty values</p></li>
<li><p>Finds better results when input is in other languages</p></li>
@@ -1171,23 +1225,25 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</li>
<li>Frequency tables (<code>freq()</code> function):
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb28"><pre class="r"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<div class="sourceCode" id="cb28"><pre class="downlit">
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<span class="co"># OLD WAY</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">genus</span>)
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(genus = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">genus</span>)
<span class="co"># NEW WAY</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>))
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
<span class="co"># Even supports grouping variables:</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">gender</span>) <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>))</pre></div>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">gender</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
</pre></div>
</li>
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
<li><p>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@@ -1257,10 +1313,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb29"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span>
<div class="sourceCode" id="cb29"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></pre></div>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span>
</pre></div>
</li>
<li><p>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></li>
<li><p>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</p></li>
@@ -1268,19 +1326,23 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code></p></li>
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
<li>
<p>Frequency tables - <code>freq()</code>:</p>
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb30"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">gender</span>)</pre></div>
<div class="sourceCode" id="cb30"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
</pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb31"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">count</span>, -<span class="no">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span></pre></div>
<div class="sourceCode" id="cb31"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">count</span>, <span class="op">-</span><span class="kw">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span>
</pre></div>
</li>
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
<li><p>Now prints in markdown at default in non-interactive sessions</p></li>
@@ -1297,7 +1359,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
@@ -1356,18 +1418,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb32"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
<div class="sourceCode" id="cb32"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] "Gram negative"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>) <span class="co"># German</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, language = <span class="st">"de"</span>) <span class="co"># German</span>
<span class="co"># [1] "Gramnegativ"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>) <span class="co"># Spanish</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, language = <span class="st">"es"</span>) <span class="co"># Spanish</span>
<span class="co"># [1] "Gram negativo"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span>
<span class="co"># [1] "Streptococcus grupo A"</span></pre></div>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, language = <span class="st">"pt"</span>) <span class="co"># Portuguese</span>
<span class="co"># [1] "Streptococcus grupo A"</span>
</pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb33"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
<div class="sourceCode" id="cb33"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
<span class="co"># [1] "Gram negative"</span></pre></div>
<span class="co"># [1] "Gram negative"</span>
</pre></div>
</li>
<li>
<p>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates</p>
@@ -1378,18 +1444,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
<div class="sourceCode" id="cb34"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
<div class="sourceCode" id="cb34"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] B_ESCHR_COL</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)
<span class="co"># [1] B_STPHY_AUR</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)
<span class="co"># [1] B_STRPTC_GRA</span></pre></div>
<span class="co"># [1] B_STRPTC_GRA</span>
</pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb35"><pre class="r"><span class="no">thousands_of_E_colis</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
<span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">thousands_of_E_colis</span>), <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"s"</span>)
<div class="sourceCode" id="cb35"><pre class="downlit">
<span class="kw">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
<span class="kw">microbenchmark</span>::<span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">thousands_of_E_colis</span>), unit = <span class="st">"s"</span>)
<span class="co"># Unit: seconds</span>
<span class="co"># min median max neval</span>
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span></pre></div>
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span>
</pre></div>
</li>
<li><p>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</p></li>
<li>
@@ -1417,12 +1487,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb36"><pre class="r"><span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
<div class="sourceCode" id="cb36"><pre class="downlit">
<span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
<span class="co"># [1] "Mupirocin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
<span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></pre></div>
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span>
</pre></div>
</li>
<li><p>For <code>first_isolate</code>, rows will be ignored when there’s no species available</p></li>
<li><p>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</p></li>
@@ -1432,13 +1504,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb37"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
<div class="sourceCode" id="cb37"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>) <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
<span class="co"># which is the same as:</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>)
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>)
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="no">amcl</span>)
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="no">amcl</span>, <span class="no">gent</span>)
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="no">amcl</span>, <span class="no">gent</span>, <span class="no">pita</span>)</pre></div>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="kw">amcl</span>)
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="kw">amcl</span>, <span class="kw">gent</span>)
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="kw">amcl</span>, <span class="kw">gent</span>, <span class="kw">pita</span>)
</pre></div>
</li>
<li><p>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</p></li>
<li><p>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</p></li>
@@ -1450,12 +1524,16 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb38"><pre class="r"><span class="no">my_matrix</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="no">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">age</span>, <span class="no">gender</span>), <span class="kw">ncol</span> <span class="kw">=</span> <span class="fl">2</span>))
<span class="fu">freq</span>(<span class="no">my_matrix</span>)</pre></div>
<div class="sourceCode" id="cb38"><pre class="downlit">
<span class="kw">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="kw">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">age</span>, <span class="kw">gender</span>), ncol = <span class="fl">2</span>))
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_matrix</span>)
</pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb39"><pre class="r"><span class="no">my_list</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw">age</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">age</span>, <span class="kw">gender</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">gender</span>)
<span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">age</span>)
<span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">gender</span>)</pre></div>
<div class="sourceCode" id="cb39"><pre class="downlit">
<span class="kw">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(age = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">age</span>, gender = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">gender</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
</pre></div>
</li>
</ul>
</div>
@@ -1529,13 +1607,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
@@ -1700,7 +1778,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/pkgdown.css
View File

@@ -244,14 +244,14 @@ nav[data-toggle='toc'] .nav .nav > .active:focus > a {
.ref-index th {font-weight: normal;}
.ref-index td {vertical-align: top;}
.ref-index td {vertical-align: top; min-width: 100px}
.ref-index .icon {width: 40px;}
.ref-index .alias {width: 40%;}
.ref-index-icons .alias {width: calc(40% - 40px);}
.ref-index .title {width: 60%;}
.ref-arguments th {text-align: right; padding-right: 10px;}
.ref-arguments th, .ref-arguments td {vertical-align: top;}
.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
.ref-arguments .name {width: 20%;}
.ref-arguments .desc {width: 80%;}

17
docs/pkgdown.yml
View File

@@ -1,17 +1,8 @@
pandoc: 2.7.3
pkgdown: 1.5.1
pkgdown_sha: ~
articles:
AMR: AMR.html
EUCAST: EUCAST.html
MDR: MDR.html
PCA: PCA.html
SPSS: SPSS.html
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-08-10T09:44Z
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-08-10T10:37Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

16
docs/reference/AMR-deprecated.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,17 +235,17 @@
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<pre class="usage"><span class='fu'>portion_R</span>(<span class='no'>...</span>)
<pre class="usage"><span class='fu'>portion_R</span>(<span class='kw'>...</span>)
<span class='fu'>portion_IR</span>(<span class='no'>...</span>)
<span class='fu'>portion_IR</span>(<span class='kw'>...</span>)
<span class='fu'>portion_I</span>(<span class='no'>...</span>)
<span class='fu'>portion_I</span>(<span class='kw'>...</span>)
<span class='fu'>portion_SI</span>(<span class='no'>...</span>)
<span class='fu'>portion_SI</span>(<span class='kw'>...</span>)
<span class='fu'>portion_S</span>(<span class='no'>...</span>)
<span class='fu'>portion_S</span>(<span class='kw'>...</span>)
<span class='fu'>portion_df</span>(<span class='no'>...</span>)</pre>
<span class='fu'>portion_df</span>(<span class='kw'>...</span>)</pre>
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired lifecycle</h2>
@@ -275,7 +275,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

8
docs/reference/AMR.html
View File

@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>The <code>AMR</code> Package — AMR • AMR (for R)</title>
<title>The AMR Package — AMR • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="The <code>AMR</code> Package — AMR" />
<meta property="og:title" content="The AMR Package — AMR" />
<meta property="og:description" content="Welcome to the AMR package." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -297,7 +297,7 @@ The Netherlands</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/reference/WHOCC.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -272,7 +272,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

6
docs/reference/WHONET.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our <a href='example_isolates.html'>example_isolates</a> data set.</p>
</div>
<pre class="usage"><span class='no'>WHONET</span></pre>
<pre class="usage"><span class='kw'>WHONET</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -290,7 +290,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

58
docs/reference/ab_from_text.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,12 +236,12 @@
</div>
<pre class="usage"><span class='fu'>ab_from_text</span>(
<span class='no'>text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>thorough_search</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>
<span class='kw'>text</span>,
type = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
collapse = <span class='kw'>NULL</span>,
translate_ab = <span class='fl'>FALSE</span>,
thorough_search = <span class='kw'>NULL</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -312,31 +312,31 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'>ab_from_text</span>(<span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"dose"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type = <span class='st'>"dose"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type = <span class='st'>"admin"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>", "</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, collapse = <span class='st'>", "</span>)
<span class='co'># if you want to know which antibiotic groups were administered, do e.g.:</span>
<span class='no'>abx</span> <span class='kw'>&lt;-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='no'>abx</span><span class='kw'>[[</span><span class='fl'>1</span>]])
<span class='kw'>abx</span> <span class='op'>&lt;-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='kw'>abx</span>[[<span class='fl'>1</span>]])
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/reexports.html'>tibble</a></span>(<span class='kw'>clinical_text</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
<span class='st'>"started on doxy iv today"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>abx_codes</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>),
<span class='kw'>abx_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>),
<span class='kw'>abx_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>),
<span class='kw'>abx_coll</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
<span class='kw'>abx_coll_names</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>),
<span class='kw'>abx_coll_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
<span class='kw'>abx_coll_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>))
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='fu'><a href='https://tibble.tidyverse.org/reference/tibble.html'>tibble</a></span>(clinical_text = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
<span class='st'>"started on doxy iv today"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(abx_codes = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>),
abx_doses = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, type = <span class='st'>"doses"</span>),
abx_admin = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, type = <span class='st'>"admin"</span>),
abx_coll = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, collapse = <span class='st'>"|"</span>),
abx_coll_names = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
collapse = <span class='st'>"|"</span>,
translate_ab = <span class='st'>"name"</span>),
abx_coll_doses = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
type = <span class='st'>"doses"</span>,
collapse = <span class='st'>"|"</span>),
abx_coll_admin = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
type = <span class='st'>"admin"</span>,
collapse = <span class='st'>"|"</span>))
}</pre>
</div>
@@ -354,7 +354,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

40
docs/reference/ab_property.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,31 +235,31 @@
<p>Use these functions to return a specific property of an antibiotic from the <a href='antibiotics.html'>antibiotics</a> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>ab_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>ab_name</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), tolower = <span class='fl'>FALSE</span>, <span class='kw'>...</span>)
<span class='fu'>ab_atc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_atc</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>ab_cid</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_cid</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>ab_synonyms</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_synonyms</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>ab_tradenames</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_tradenames</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>ab_group</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_group</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>ab_atc_group1</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_atc_group1</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>ab_atc_group2</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_atc_group2</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>ab_loinc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_loinc</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>ab_ddd</span>(<span class='no'>x</span>, <span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>ab_ddd</span>(<span class='kw'>x</span>, administration = <span class='st'>"oral"</span>, units = <span class='fl'>FALSE</span>, <span class='kw'>...</span>)
<span class='fu'>ab_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_info</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>ab_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>ab_url</span>(<span class='kw'>x</span>, open = <span class='fl'>FALSE</span>, <span class='kw'>...</span>)
<span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
<span class='fu'>ab_property</span>(<span class='kw'>x</span>, property = <span class='st'>"name"</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -348,15 +348,15 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>ab_url</span>(<span class='st'>"AMX"</span>) <span class='co'># link to the official WHO page</span>
<span class='co'># smart lowercase tranformation</span>
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>)) <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>),
<span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
<span class='fu'>ab_name</span>(x = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>)) <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
<span class='fu'>ab_name</span>(x = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>),
tolower = <span class='fl'>TRUE</span>) <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
<span class='co'># defined daily doses (DDD)</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>) <span class='co'># 1</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, units = <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>) <span class='co'># 1</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>, units = <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
<span class='fu'>ab_info</span>(<span class='st'>"AMX"</span>) <span class='co'># all properties as a list</span>
@@ -388,7 +388,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

14
docs/reference/age.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>Calculates age in years based on a reference date, which is the sytem date at default.</p>
</div>
<pre class="usage"><span class='fu'>age</span>(<span class='no'>x</span>, <span class='kw'>reference</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), <span class='kw'>exact</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<pre class="usage"><span class='fu'>age</span>(<span class='kw'>x</span>, reference = <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), exact = <span class='fl'>FALSE</span>, na.rm = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -279,13 +279,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># 10 random birth dates</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>birth_date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>() - <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span>(<span class='fl'>10</span>) * <span class='fl'>25000</span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(birth_date = <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>() <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span>(<span class='fl'>10</span>) <span class='op'>*</span> <span class='fl'>25000</span>)
<span class='co'># add ages</span>
<span class='no'>df</span>$<span class='no'>age</span> <span class='kw'>&lt;-</span> <span class='fu'>age</span>(<span class='no'>df</span>$<span class='no'>birth_date</span>)
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>age</span> <span class='op'>&lt;-</span> <span class='fu'>age</span>(<span class='kw'>df</span><span class='op'>$</span><span class='kw'>birth_date</span>)
<span class='co'># add exact ages</span>
<span class='no'>df</span>$<span class='no'>age_exact</span> <span class='kw'>&lt;-</span> <span class='fu'>age</span>(<span class='no'>df</span>$<span class='no'>birth_date</span>, <span class='kw'>exact</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>age_exact</span> <span class='op'>&lt;-</span> <span class='fu'>age</span>(<span class='kw'>df</span><span class='op'>$</span><span class='kw'>birth_date</span>, exact = <span class='fl'>TRUE</span>)
<span class='no'>df</span></pre>
<span class='kw'>df</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -301,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

40
docs/reference/age_groups.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>Split ages into age groups defined by the <code>split</code> parameter. This allows for easier demographic (antimicrobial resistance) analysis.</p>
</div>
<pre class="usage"><span class='fu'>age_groups</span>(<span class='no'>x</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<pre class="usage"><span class='fu'>age_groups</span>(<span class='kw'>x</span>, split_at = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span>), na.rm = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -287,36 +287,36 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>ages</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
<pre class="examples"><span class='kw'>ages</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
<span class='co'># split into 0-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fl'>50</span>)
<span class='co'># split into 0-19, 20-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
<span class='co'># split into groups of ten years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>10</span> <span class='op'>*</span> <span class='fl'>10</span>)
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, split_at = <span class='st'>"tens"</span>)
<span class='co'># split into groups of five years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>20</span> <span class='op'>*</span> <span class='fl'>5</span>)
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, split_at = <span class='st'>"fives"</span>)
<span class='co'># split specifically for children</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='st'>"children"</span>)
<span class='co'># same:</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(age_group = <span class='fu'>age_groups</span>(<span class='kw'>age</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>age_group</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(x = <span class='st'>"age_group"</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -333,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

44
docs/reference/antibiotic_class_selectors.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>Use these selection helpers inside any function that allows <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selections</a>, like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>dplyr::select()</a></code> or <code><a href='https://tidyr.tidyverse.org/reference/pivot_longer.html'>tidyr::pivot_longer()</a></code>. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>ab_class</span>(<span class='no'>ab_class</span>)
<pre class="usage"><span class='fu'>ab_class</span>(<span class='kw'>ab_class</span>)
<span class='fu'>aminoglycosides</span>()
@@ -281,32 +281,32 @@
<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>carbapenems</span>())
<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>aminoglycosides</span>())
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>aminoglycosides</span>())
<span class='co'># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>ab_class</span>(<span class='st'>"mycobact"</span>))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>ab_class</span>(<span class='st'>"mycobact"</span>))
<span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>"pos"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>macrolides</span>()) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span>() <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"pos"</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>macrolides</span>()) <span class='op'>%&gt;%</span>
<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span>() <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>()
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>irrelevant</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
<span class='kw'>J01CA01</span> <span class='kw'>=</span> <span class='st'>"S"</span>) <span class='kw'>%&gt;%</span> <span class='co'># ATC code of ampicillin</span>
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(irrelevant = <span class='st'>"value"</span>,
J01CA01 = <span class='st'>"S"</span>) <span class='op'>%&gt;%</span> <span class='co'># ATC code of ampicillin</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>()) <span class='co'># so the 'J01CA01' column is selected</span>
}</pre>
@@ -325,7 +325,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

8
docs/reference/antibiotics.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,9 +235,9 @@
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href='as.ab.html'>as.ab()</a></code> or one of the <code><a href='ab_property.html'>ab_property()</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes.</p>
</div>
<pre class="usage"><span class='no'>antibiotics</span>
<pre class="usage"><span class='kw'>antibiotics</span>
<span class='no'>antivirals</span></pre>
<span class='kw'>antivirals</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -334,7 +334,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

8
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@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,9 +235,9 @@
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
</div>
<pre class="usage"><span class='fu'>as.ab</span>(<span class='no'>x</span>, <span class='kw'>flag_multiple_results</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>as.ab</span>(<span class='kw'>x</span>, flag_multiple_results = <span class='fl'>TRUE</span>, <span class='kw'>...</span>)
<span class='fu'>is.ab</span>(<span class='no'>x</span>)</pre>
<span class='fu'>is.ab</span>(<span class='kw'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -344,7 +344,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

38
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View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,9 +235,9 @@
<p>This transforms a vector to a new class <code>disk</code>, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<pre class="usage"><span class='fu'>as.disk</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>as.disk</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='fu'>is.disk</span>(<span class='no'>x</span>)</pre>
<span class='fu'>is.disk</span>(<span class='kw'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -275,24 +275,24 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># transform existing disk zones to the `disk` class</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fl'>20</span>,
<span class='kw'>CIP</span> <span class='kw'>=</span> <span class='fl'>14</span>,
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fl'>18</span>,
<span class='kw'>TOB</span> <span class='kw'>=</span> <span class='fl'>16</span>)
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.disk</span>)
<span class='no'>df</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(microorganism = <span class='st'>"E. coli"</span>,
AMP = <span class='fl'>20</span>,
CIP = <span class='fl'>14</span>,
GEN = <span class='fl'>18</span>,
TOB = <span class='fl'>16</span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.disk</span>)
<span class='kw'>df</span>
<span class='co'># interpret disk values, see ?as.rsi</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.disk</span>(<span class='fl'>18</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='no'>df</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(x = <span class='fu'>as.disk</span>(<span class='fl'>18</span>),
mo = <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
ab = <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>df</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -309,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

32
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View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,9 +235,9 @@
<p>This transforms a vector to a new class <code>mic</code>, which is an ordered <code><a href='https://rdrr.io/r/base/factor.html'>factor</a></code> with valid MIC values as levels. Invalid MIC values will be translated as <code>NA</code> with a warning.</p>
</div>
<pre class="usage"><span class='fu'>as.mic</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>as.mic</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='fu'>is.mic</span>(<span class='no'>x</span>)</pre>
<span class='fu'>is.mic</span>(<span class='kw'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -275,24 +275,24 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>mic_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mic</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&gt;=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"&lt;=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span>))
<span class='fu'>is.mic</span>(<span class='no'>mic_data</span>)
<pre class="examples"><span class='kw'>mic_data</span> <span class='op'>&lt;-</span> <span class='fu'>as.mic</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&gt;=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"&lt;=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span>))
<span class='fu'>is.mic</span>(<span class='kw'>mic_data</span>)
<span class='co'># this can also coerce combined MIC/RSI values:</span>
<span class='fu'>as.mic</span>(<span class='st'>"&lt;=0.002; S"</span>) <span class='co'># will return &lt;=0.002</span>
<span class='co'># interpret MIC values</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.mic</span>(<span class='fl'>2</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.mic</span>(<span class='fl'>4</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(x = <span class='fu'>as.mic</span>(<span class='fl'>2</span>),
mo = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
ab = <span class='st'>"AMX"</span>,
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(x = <span class='fu'>as.mic</span>(<span class='fl'>4</span>),
mo = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
ab = <span class='st'>"AMX"</span>,
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>mic_data</span>)</pre>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>mic_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>mic_data</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -308,7 +308,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

48
docs/reference/as.mo.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,15 +236,15 @@
</div>
<pre class="usage"><span class='fu'>as.mo</span>(
<span class='no'>x</span>,
<span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
<span class='no'>...</span>
<span class='kw'>x</span>,
Becker = <span class='fl'>FALSE</span>,
Lancefield = <span class='fl'>FALSE</span>,
allow_uncertain = <span class='fl'>TRUE</span>,
reference_df = <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
<span class='kw'>...</span>
)
<span class='fu'>is.mo</span>(<span class='no'>x</span>)
<span class='fu'>is.mo</span>(<span class='kw'>x</span>)
<span class='fu'>mo_failures</span>()
@@ -299,10 +299,10 @@
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---&amp;gt; subspecies, a 4-5 letter acronym
| | ----&amp;gt; species, a 4-5 letter acronym
| ----&amp;gt; genus, a 5-7 letter acronym
----&amp;gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
| | | ---&gt; subspecies, a 4-5 letter acronym
| | ----&gt; species, a 4-5 letter acronym
| ----&gt; genus, a 5-7 letter acronym
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>
@@ -412,32 +412,32 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPDR</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CONS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CONS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYGN</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRPA</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRPA</span>
<span class='co'># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Gram negative"</span>
<span class='co'># }</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='no'>df</span>$<span class='no'>microorganism_name</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>mo</span> <span class='op'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='kw'>df</span><span class='op'>$</span><span class='kw'>microorganism_name</span>)
<span class='co'># the select function of the Tidyverse is also supported:</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>mo</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>microorganism_name</span>) <span class='op'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%&gt;%</span>
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>mo</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>genus</span>, <span class='kw'>species</span>) <span class='op'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># although this works easier and does the same:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(mo = <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='kw'>genus</span>, <span class='kw'>species</span>)))
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -454,7 +454,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

149
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View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,41 +235,41 @@
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Values that cannot be interpreted will be returned as <code>NA</code> with a warning.</p>
</div>
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
<span class='fu'>is.rsi</span>(<span class='kw'>x</span>)
<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>x</span>, threshold = <span class='fl'>0.05</span>)
<span class='co'># S3 method for mic</span>
<span class='fu'>as.rsi</span>(
<span class='no'>x</span>,
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)),
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
mo = <span class='kw'>NULL</span>,
ab = <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>)),
guideline = <span class='st'>"EUCAST"</span>,
uti = <span class='fl'>FALSE</span>,
conserve_capped_values = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='co'># S3 method for disk</span>
<span class='fu'>as.rsi</span>(
<span class='no'>x</span>,
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)),
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
mo = <span class='kw'>NULL</span>,
ab = <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>)),
guideline = <span class='st'>"EUCAST"</span>,
uti = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='co'># S3 method for data.frame</span>
<span class='fu'>as.rsi</span>(
<span class='no'>x</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_mo = <span class='kw'>NULL</span>,
guideline = <span class='st'>"EUCAST"</span>,
uti = <span class='kw'>NULL</span>,
conserve_capped_values = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -325,13 +325,13 @@
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.mic</span>, <span class='no'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='no'>is.mic</span>), <span class='no'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.mic</span>, <span class='kw'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.disk</span>, <span class='no'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='no'>is.disk</span>), <span class='no'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.disk</span>, <span class='kw'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.disk</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
</ol>
@@ -389,53 +389,54 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
<span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
<span class='co'># a whole data set, even with combined MIC values and disk zones</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>8</span>),
<span class='kw'>CIP</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>0.256</span>),
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
<span class='kw'>TOB</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>16</span>),
<span class='kw'>NIT</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>32</span>))
<span class='fu'>as.rsi</span>(<span class='no'>df</span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(microorganism = <span class='st'>"E. coli"</span>,
AMP = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>8</span>),
CIP = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>0.256</span>),
GEN = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
TOB = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>16</span>),
NIT = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>32</span>))
<span class='fu'>as.rsi</span>(<span class='kw'>df</span>)
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># the dplyr way</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>)
<span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>)
<span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>)
<span class='co'># to include information about urinary tract infections (UTI)</span>
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
<span class='kw'>NIT</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
<span class='kw'>from_the_bladder</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>TRUE</span>, <span class='fl'>FALSE</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>as.rsi</span>(<span class='kw'>uti</span> <span class='kw'>=</span> <span class='st'>"from_the_bladder"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
<span class='kw'>NIT</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
<span class='kw'>specimen</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"urine"</span>, <span class='st'>"blood"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
from_the_bladder = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>TRUE</span>, <span class='fl'>FALSE</span>)) <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>(uti = <span class='st'>"from_the_bladder"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
specimen = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"urine"</span>, <span class='st'>"blood"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>() <span class='co'># automatically determines urine isolates</span>
<span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>NIT</span>), <span class='no'>as.rsi</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>NIT</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>, uti = <span class='fl'>TRUE</span>)
}
<span class='co'># for single values</span>
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMP"</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'>as.rsi</span>(x = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
mo = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
ab = <span class='st'>"AMP"</span>,
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'>as.rsi</span>(x = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
mo = <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
ab = <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline = <span class='st'>"EUCAST"</span>)
<span class='co'># For CLEANING existing R/SI values ------------------------------------</span>
@@ -443,27 +444,27 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>, <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span>))
<span class='fu'>as.rsi</span>(<span class='st'>"&lt;= 0.002; S"</span>) <span class='co'># will return "S"</span>
<span class='no'>rsi_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
<span class='fu'>is.rsi</span>(<span class='no'>rsi_data</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
<span class='kw'>rsi_data</span> <span class='op'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
<span class='fu'>is.rsi</span>(<span class='kw'>rsi_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for frequencies</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>PEN</span>:<span class='no'>RIF</span>), <span class='no'>as.rsi</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>PEN</span><span class='op'>:</span><span class='kw'>RIF</span>), <span class='kw'>as.rsi</span>)
<span class='co'># fastest way to transform all columns with already valid AMR results to class `rsi`:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>, <span class='no'>as.rsi</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.rsi.eligible</span>, <span class='kw'>as.rsi</span>)
<span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
<span class='co'># example_isolates %&gt;%</span>
<span class='co'># mutate(across(is.rsi.eligible, as.rsi))</span>
<span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.99</span>) <span class='co'># succeeds</span>
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>, threshold = <span class='fl'>0.99</span>) <span class='co'># succeeds</span>
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -480,7 +481,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

20
docs/reference/atc_online.html
View File

@@ -83,7 +83,7 @@ This function requires an internet connection." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -238,15 +238,15 @@ This function requires an internet connection." />
</div>
<pre class="usage"><span class='fu'>atc_online_property</span>(
<span class='no'>atc_code</span>,
<span class='no'>property</span>,
<span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"O"</span>,
<span class='kw'>url</span> <span class='kw'>=</span> <span class='st'>"https://www.whocc.no/atc_ddd_index/?code=%s&amp;showdescription=no"</span>
<span class='kw'>atc_code</span>,
<span class='kw'>property</span>,
administration = <span class='st'>"O"</span>,
url = <span class='st'>"https://www.whocc.no/atc_ddd_index/?code=%s&amp;showdescription=no"</span>
)
<span class='fu'>atc_online_groups</span>(<span class='no'>atc_code</span>, <span class='no'>...</span>)
<span class='fu'>atc_online_groups</span>(<span class='kw'>atc_code</span>, <span class='kw'>...</span>)
<span class='fu'>atc_online_ddd</span>(<span class='no'>atc_code</span>, <span class='no'>...</span>)</pre>
<span class='fu'>atc_online_ddd</span>(<span class='kw'>atc_code</span>, <span class='kw'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -315,13 +315,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
<span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span>)
<span class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
<span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span>)
<span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"groups"</span>) <span class='co'># search hierarchical groups of amoxicillin</span>
<span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, property = <span class='st'>"groups"</span>) <span class='co'># search hierarchical groups of amoxicillin</span>
<span class='co'># [1] "ANTIINFECTIVES FOR SYSTEMIC USE"</span>
<span class='co'># [2] "ANTIBACTERIALS FOR SYSTEMIC USE"</span>
<span class='co'># [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
@@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

24
docs/reference/availability.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. <code><a href='proportion.html'>susceptibility()</a></code> and <code><a href='proportion.html'>resistance()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>availability</span>(<span class='no'>tbl</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
<pre class="usage"><span class='fu'>availability</span>(<span class='kw'>tbl</span>, width = <span class='kw'>NULL</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -270,19 +270,19 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>availability</span>(<span class='no'>example_isolates</span>)
<pre class="examples"><span class='fu'>availability</span>(<span class='kw'>example_isolates</span>)
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>availability</span>()
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>availability</span>()
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='no'>is.rsi</span>) <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='kw'>is.rsi</span>) <span class='op'>%&gt;%</span>
<span class='fu'>availability</span>()
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='no'>is.rsi</span>) <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='kw'>is.rsi</span>) <span class='op'>%&gt;%</span>
<span class='fu'>availability</span>()
}</pre>
</div>
@@ -300,7 +300,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

44
docs/reference/bug_drug_combinations.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,21 +235,21 @@
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publicable/printable format, see Examples.</p>
</div>
<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_shortname</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='kw'>x</span>, col_mo = <span class='kw'>NULL</span>, FUN = <span class='kw'>mo_shortname</span>, <span class='kw'>...</span>)
<span class='co'># S3 method for bug_drug_combinations</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(
<span class='no'>x</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name (ab, atc)"</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>remove_intrinsic_resistant</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"OutDec"</span>),
<span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>),
<span class='no'>...</span>
<span class='kw'>x</span>,
translate_ab = <span class='st'>"name (ab, atc)"</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
minimum = <span class='fl'>30</span>,
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>,
add_ab_group = <span class='fl'>TRUE</span>,
remove_intrinsic_resistant = <span class='fl'>FALSE</span>,
decimal.mark = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"OutDec"</span>),
big.mark = <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>decimal.mark</span> <span class='op'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>),
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -337,16 +337,16 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>)
<span class='no'>x</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name (atc)"</span>)
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>)
<span class='kw'>x</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='kw'>x</span>, translate_ab = <span class='st'>"name (atc)"</span>)
<span class='co'># Use FUN to change to transformation of microorganism codes</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>,
<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_gramstain</span>)
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>,
<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>x</span> <span class='kw'>==</span> <span class='st'>"B_ESCHR_COLI"</span>,
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='kw'>mo_gramstain</span>)
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
FUN = <span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>x</span> <span class='op'>==</span> <span class='st'>"B_ESCHR_COLI"</span>,
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span>))
<span class='co'># }</span></pre>
@@ -365,7 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/reference/catalogue_of_life.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -313,7 +313,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/reference/catalogue_of_life_version.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -275,7 +275,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

133
docs/reference/count.html
View File

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -233,34 +233,34 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</div>
<div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>summarise()</code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</p>
</div>
<pre class="usage"><span class='fu'>count_resistant</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>count_resistant</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_susceptible</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_susceptible</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_R</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_IR</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_IR</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_I</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_I</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_SI</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_SI</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_S</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_S</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_all</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_all</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>n_rsi</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>n_rsi</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_df</span>(
<span class='no'>data</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
<span class='kw'>data</span>,
translate_ab = <span class='st'>"name"</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -338,22 +338,21 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
-------- -------- ---------- ----------- ---------- -----------
S or I S or I X X X X
R S or I X X X X
&amp;lt;NA&amp;gt; S or I X X - -
&lt;NA&gt; S or I X X - -
S or I R X X X X
R R - X - X
&amp;lt;NA&amp;gt; R - - - -
S or I &amp;lt;NA&amp;gt; X X - -
R &amp;lt;NA&amp;gt; - - - -
&amp;lt;NA&amp;gt; &amp;lt;NA&amp;gt; - - - -
&lt;NA&gt; R - - - -
S or I &lt;NA&gt; X X - -
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() + <span class='fu'>count_I</span>() + <span class='fu'>count_R</span>() <span class='kw'>=</span> <span class='fu'>count_all</span>()
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() + <span class='fu'><a href='proportion.html'>proportion_I</a></span>() + <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>=</span> <span class='fu'>count_all</span>()
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='op'>=</span> <span class='fl'>1</span></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &amp;gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &amp;gt;= 1
</pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>&gt;=</span> <span class='fu'>count_all</span>()
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='op'>&gt;=</span> <span class='fl'>1</span></pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@@ -367,63 +366,63 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
?<span class='no'>example_isolates</span>
<span class='op'>?</span><span class='kw'>example_isolates</span>
<span class='fu'>count_resistant</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "R"</span>
<span class='fu'>count_susceptible</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "S" and "I"</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "S", "I" and "R"</span>
<span class='fu'>count_resistant</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "R"</span>
<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S" and "I"</span>
<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S", "I" and "R"</span>
<span class='co'># be more specific</span>
<span class='fu'>count_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_I</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='co'># Count all available isolates</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='co'># n_rsi() is an alias of count_all().</span>
<span class='co'># Since it counts all available isolates, you can</span>
<span class='co'># calculate back to count e.g. susceptible isolates.</span>
<span class='co'># These results are the same:</span>
<span class='fu'>count_susceptible</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='op'>*</span> <span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>CIP</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>CIP</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>CIP</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(R = <span class='fu'>count_R</span>(<span class='kw'>CIP</span>),
I = <span class='fu'>count_I</span>(<span class='kw'>CIP</span>),
S = <span class='fu'>count_S</span>(<span class='kw'>CIP</span>),
n1 = <span class='fu'>count_all</span>(<span class='kw'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
n2 = <span class='fu'>n_rsi</span>(<span class='kw'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
total = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
<span class='co'># Please mind that `susceptibility()` calculates percentages right away instead.</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>AMC</span>) <span class='co'># 1433</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>AMC</span>) <span class='co'># 1879</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>GEN</span>) <span class='co'># 1399</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>GEN</span>) <span class='co'># 1855</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># 1764</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># 1936</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>) <span class='co'># 1433</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>) <span class='co'># 1879</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>GEN</span>) <span class='co'># 1399</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='kw'>GEN</span>) <span class='co'># 1855</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1764</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1936</span>
<span class='co'># Get number of S+I vs. R immediately of selected columns</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>count_df</span>(translate = <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'>count_df</span>(translate = <span class='fl'>FALSE</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -440,7 +439,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

42
docs/reference/eucast_rules.html
View File

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -238,12 +238,12 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</div>
<pre class="usage"><span class='fu'>eucast_rules</span>(
<span class='no'>x</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR.eucast_rules"</span>, <span class='kw'>default</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_mo = <span class='kw'>NULL</span>,
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR.eucast_rules"</span>, default = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
verbose = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -407,21 +407,21 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='kw'>a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
<span class='st'>"Klebsiella pneumoniae"</span>,
<span class='st'>"Pseudomonas aeruginosa"</span>),
<span class='kw'>VAN</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
<span class='kw'>AMX</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
<span class='kw'>COL</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
<span class='kw'>CAZ</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
<span class='kw'>CXM</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
<span class='kw'>PEN</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Penicillin G</span>
<span class='kw'>FOX</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
VAN = <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
AMX = <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
COL = <span class='st'>"-"</span>, <span class='co'># Colistin</span>
CAZ = <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
CXM = <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
PEN = <span class='st'>"S"</span>, <span class='co'># Penicillin G</span>
FOX = <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
stringsAsFactors = <span class='fl'>FALSE</span>)
<span class='no'>a</span>
<span class='kw'>a</span>
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
@@ -431,9 +431,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># apply EUCAST rules: 18 results are forced as R or S</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>)
<span class='kw'>b</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>)
<span class='no'>b</span>
<span class='kw'>b</span>
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
@@ -444,7 +444,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
<span class='co'># with 18 rows, containing all details about the transformations:</span>
<span class='no'>c</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='kw'>c</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>, verbose = <span class='fl'>TRUE</span>)
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -461,7 +461,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
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6
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View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read <a href='https://msberends.github.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
</div>
<pre class="usage"><span class='no'>example_isolates</span></pre>
<pre class="usage"><span class='kw'>example_isolates</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -274,7 +274,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

6
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@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.</p>
</div>
<pre class="usage"><span class='no'>example_isolates_unclean</span></pre>
<pre class="usage"><span class='kw'>example_isolates_unclean</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -269,7 +269,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

62
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View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,33 +235,33 @@
<p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.</p>
</div>
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='no'>x</span>, <span class='no'>ab_class</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='kw'>x</span>, <span class='kw'>ab_class</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_aminoglycosides</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_aminoglycosides</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_carbapenems</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_carbapenems</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_cephalosporins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_1st_cephalosporins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_1st_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_2nd_cephalosporins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_2nd_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_3rd_cephalosporins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_3rd_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_4th_cephalosporins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_4th_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_5th_cephalosporins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_5th_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_fluoroquinolones</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_fluoroquinolones</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_glycopeptides</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_glycopeptides</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_macrolides</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_macrolides</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_penicillins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_penicillins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_tetracyclines</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)</pre>
<span class='fu'>filter_tetracyclines</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -303,40 +303,40 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='antibiotic_class_selectors.html'>antibiotic_class_selectors()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='co'># filter on isolates that have any result for any aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>()
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>()
<span class='co'># this is essentially the same as (but without determination of column names):</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></span>(<span class='kw'>.vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"GEN"</span>, <span class='st'>"TOB"</span>, <span class='st'>"AMK"</span>, <span class='st'>"KAN"</span>)),
<span class='kw'>.vars_predicate</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/all_vars.html'>any_vars</a></span>(<span class='no'>.</span> <span class='kw'>%in%</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>)))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></span>(.vars = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"GEN"</span>, <span class='st'>"TOB"</span>, <span class='st'>"AMK"</span>, <span class='st'>"KAN"</span>)),
.vars_predicate = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/all_vars.html'>any_vars</a></span>(<span class='kw'>.</span> <span class='op'>%in%</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>)))
<span class='co'># filter on isolates that show resistance to ANY aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
<span class='co'># filter on isolates that show resistance to ALL aminoglycosides</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='co'># filter on isolates that show resistance to</span>
<span class='co'># any aminoglycoside and any fluoroquinolone</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>) <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>) <span class='op'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>)
<span class='co'># filter on isolates that show resistance to</span>
<span class='co'># all aminoglycosides and all fluoroquinolones</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='op'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_carbapenems</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span>(), ~<span class='no'>.</span> <span class='kw'>==</span> <span class='st'>"R"</span>))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_carbapenems</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span>(), <span class='op'>~</span><span class='kw'>.</span> <span class='op'>==</span> <span class='st'>"R"</span>))
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -353,7 +353,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

118
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View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,41 +236,41 @@
</div>
<pre class="usage"><span class='fu'>first_isolate</span>(
<span class='no'>x</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_testcode</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_specimen</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_icu</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>episode_days</span> <span class='kw'>=</span> <span class='fl'>365</span>,
<span class='kw'>testcodes_exclude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>icu_exclude</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"keyantibiotics"</span>,
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>include_unknown</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_date = <span class='kw'>NULL</span>,
col_patient_id = <span class='kw'>NULL</span>,
col_mo = <span class='kw'>NULL</span>,
col_testcode = <span class='kw'>NULL</span>,
col_specimen = <span class='kw'>NULL</span>,
col_icu = <span class='kw'>NULL</span>,
col_keyantibiotics = <span class='kw'>NULL</span>,
episode_days = <span class='fl'>365</span>,
testcodes_exclude = <span class='kw'>NULL</span>,
icu_exclude = <span class='fl'>FALSE</span>,
specimen_group = <span class='kw'>NULL</span>,
type = <span class='st'>"keyantibiotics"</span>,
ignore_I = <span class='fl'>TRUE</span>,
points_threshold = <span class='fl'>2</span>,
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
include_unknown = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='fu'>filter_first_isolate</span>(
<span class='no'>x</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_date = <span class='kw'>NULL</span>,
col_patient_id = <span class='kw'>NULL</span>,
col_mo = <span class='kw'>NULL</span>,
<span class='kw'>...</span>
)
<span class='fu'>filter_first_weighted_isolate</span>(
<span class='no'>x</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_date = <span class='kw'>NULL</span>,
col_patient_id = <span class='kw'>NULL</span>,
col_mo = <span class='kw'>NULL</span>,
col_keyantibiotics = <span class='kw'>NULL</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -362,14 +362,14 @@
<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode <a href='https://www.ncbi.nlm.nih.gov/pubmed/17304462'>(ref)</a>. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all <em>S. aureus</em> isolates would be overestimated, because you included this MRSA more than once. It would be <a href='https://en.wikipedia.org/wiki/Selection_bias'>selection bias</a>.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p>
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate()</code> is essentially equal to one of:</p><pre> <span class='no'>x</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'>first_isolate</span>(<span class='no'>.</span>, <span class='no'>...</span>))</pre>
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate()</code> is essentially equal to one of:</p><pre> <span class='kw'>x</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'>first_isolate</span>(<span class='kw'>.</span>, <span class='kw'>...</span>))</pre>
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> <span class='no'>x</span> <span class='kw'>%&amp;gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>.</span>)) <span class='kw'>%&amp;gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>only_weighted_firsts</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>"keyab"</span>, <span class='no'>...</span>)) <span class='kw'>%&amp;gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>only_weighted_firsts</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&amp;gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>only_weighted_firsts</span>, -<span class='no'>keyab</span>)</pre>
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> <span class='kw'>x</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(keyab = <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='kw'>.</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(only_weighted_firsts = <span class='fu'>first_isolate</span>(<span class='kw'>x</span>,
col_keyantibiotics = <span class='st'>"keyab"</span>, <span class='kw'>...</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>only_weighted_firsts</span> <span class='op'>==</span> <span class='fl'>TRUE</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='op'>-</span><span class='kw'>only_weighted_firsts</span>, <span class='op'>-</span><span class='kw'>keyab</span>)</pre>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
@@ -402,24 +402,24 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='co'># Filter on first isolates:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(first_isolate = <span class='fu'>first_isolate</span>(<span class='kw'>.</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>first_isolate</span> <span class='op'>==</span> <span class='fl'>TRUE</span>)
<span class='co'># Now let's see if first isolates matter:</span>
<span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='kw'>A</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(count = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>GEN</span>), <span class='co'># gentamicin availability</span>
resistance = <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='kw'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='kw'>B</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='op'>%&gt;%</span> <span class='co'># the 1st isolate filter</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(count = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>GEN</span>), <span class='co'># gentamicin availability</span>
resistance = <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='kw'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='co'># Have a look at A and B.</span>
<span class='co'># B is more reliable because every isolate is counted only once.</span>
@@ -430,21 +430,21 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'>## OTHER EXAMPLES:</span>
<span class='co'># Short-hand versions:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_first_isolate</span>()
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>()
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>x</span>$<span class='no'>keyab</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>x</span>)
<span class='kw'>x</span><span class='op'>$</span><span class='kw'>keyab</span> <span class='op'>&lt;-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='kw'>x</span>)
<span class='no'>x</span>$<span class='no'>first_isolate</span> <span class='kw'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>)
<span class='kw'>x</span><span class='op'>$</span><span class='kw'>first_isolate</span> <span class='op'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='kw'>x</span>)
<span class='no'>x</span>$<span class='no'>first_isolate_weighed</span> <span class='kw'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='kw'>x</span><span class='op'>$</span><span class='kw'>first_isolate_weighed</span> <span class='op'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='kw'>x</span>, col_keyantibiotics = <span class='st'>'keyab'</span>)
<span class='no'>x</span>$<span class='no'>first_blood_isolate</span> <span class='kw'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>, <span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>"Blood"</span>)
<span class='kw'>x</span><span class='op'>$</span><span class='kw'>first_blood_isolate</span> <span class='op'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='kw'>x</span>, specimen_group = <span class='st'>"Blood"</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -461,7 +461,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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23
docs/reference/g.test.html
View File

@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title><em>G</em>-test for Count Data — g.test • AMR (for R)</title>
<title>G-test for Count Data — g.test • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="<em>G</em>-test for Count Data — g.test" />
<meta property="og:title" content="G-test for Count Data — g.test" />
<meta property="og:description" content="g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable (1). A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence)." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p><code>g.test()</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code> but is more reliable (1). A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
</div>
<pre class="usage"><span class='fu'>g.test</span>(<span class='no'>x</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>/<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>x</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>x</span>)), <span class='kw'>rescale.p</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<pre class="usage"><span class='fu'>g.test</span>(<span class='kw'>x</span>, y = <span class='kw'>NULL</span>, p = <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='kw'>x</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='kw'>x</span>)), rescale.p = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -319,7 +319,7 @@
<p>Unlike the exact test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
<p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
<p>\(G = 2 * sum(x * log(x / E))\)</p>
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre><span class='no'>p</span> <span class='kw'>&amp;</span><span class='no'>lt</span>;- <span class='kw pkg'>stats</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span>(<span class='no'>G</span>, <span class='no'>df</span>, <span class='kw'>lower.tail</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre><span class='kw'>p</span> <span class='op'>&lt;-</span> <span class='kw'>stats</span>::<span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span>(<span class='kw'>G</span>, <span class='kw'>df</span>, lower.tail = <span class='fl'>FALSE</span>)</pre>
<p>where <code>df</code> are the degrees of freedom.</p>
<p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
@@ -356,8 +356,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># by a single gene with two co-dominant alleles, you would expect a 1:2:1</span>
<span class='co'># ratio.</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>772</span>, <span class='fl'>1611</span>, <span class='fl'>737</span>)
<span class='no'>G</span> <span class='kw'>&lt;-</span> <span class='fu'>g.test</span>(<span class='no'>x</span>, <span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>1</span>) / <span class='fl'>4</span>)
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>772</span>, <span class='fl'>1611</span>, <span class='fl'>737</span>)
<span class='kw'>G</span> <span class='op'>&lt;-</span> <span class='fu'>g.test</span>(<span class='kw'>x</span>, p = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>1</span>) <span class='op'>/</span> <span class='fl'>4</span>)
<span class='co'># G$p.value = 0.12574.</span>
<span class='co'># There is no significant difference from a 1:2:1 ratio.</span>
@@ -372,12 +372,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992)</span>
<span class='co'># observed 1752 right-billed and 1895 left-billed crossbills.</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1752</span>, <span class='fl'>1895</span>)
<span class='fu'>g.test</span>(<span class='no'>x</span>)
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1752</span>, <span class='fl'>1895</span>)
<span class='fu'>g.test</span>(<span class='kw'>x</span>)
<span class='co'># p = 0.01787343</span>
<span class='co'># There is a significant difference from a 1:1 ratio.</span>
<span class='co'># Meaning: there are significantly more left-billed birds.</span></pre>
<span class='co'># Meaning: there are significantly more left-billed birds.</span>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -393,7 +394,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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84
docs/reference/ggplot_pca.html
View File

@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>PCA biplot with <code>ggplot2</code> — ggplot_pca • AMR (for R)</title>
<title>PCA biplot with ggplot2 — ggplot_pca • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="PCA biplot with <code>ggplot2</code> — ggplot_pca" />
<meta property="og:title" content="PCA biplot with ggplot2 — ggplot_pca" />
<meta property="og:description" content="Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,28 +236,28 @@
</div>
<pre class="usage"><span class='fu'>ggplot_pca</span>(
<span class='no'>x</span>,
<span class='kw'>choices</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>2</span>,
<span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>pc.biplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>labels</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>labels_textsize</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>labels_text_placement</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
<span class='kw'>groups</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>ellipse</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>ellipse_prob</span> <span class='kw'>=</span> <span class='fl'>0.68</span>,
<span class='kw'>ellipse_size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>ellipse_alpha</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>points_size</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>points_alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>,
<span class='kw'>arrows</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>arrows_colour</span> <span class='kw'>=</span> <span class='st'>"darkblue"</span>,
<span class='kw'>arrows_size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>arrows_textsize</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>arrows_textangled</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>arrows_alpha</span> <span class='kw'>=</span> <span class='fl'>0.75</span>,
<span class='kw'>base_textsize</span> <span class='kw'>=</span> <span class='fl'>10</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
choices = <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>,
scale = <span class='fl'>TRUE</span>,
pc.biplot = <span class='fl'>TRUE</span>,
labels = <span class='kw'>NULL</span>,
labels_textsize = <span class='fl'>3</span>,
labels_text_placement = <span class='fl'>1.5</span>,
groups = <span class='kw'>NULL</span>,
ellipse = <span class='fl'>TRUE</span>,
ellipse_prob = <span class='fl'>0.68</span>,
ellipse_size = <span class='fl'>0.5</span>,
ellipse_alpha = <span class='fl'>0.5</span>,
points_size = <span class='fl'>2</span>,
points_alpha = <span class='fl'>0.25</span>,
arrows = <span class='fl'>TRUE</span>,
arrows_colour = <span class='st'>"darkblue"</span>,
arrows_size = <span class='fl'>0.5</span>,
arrows_textsize = <span class='fl'>3</span>,
arrows_textangled = <span class='fl'>TRUE</span>,
arrows_alpha = <span class='fl'>0.75</span>,
base_textsize = <span class='fl'>10</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -388,24 +388,24 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># See ?example_isolates.</span>
<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>pca_model</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='pca.html'>pca</a></span>(<span class='no'>FLC</span>, <span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>, <span class='no'>CIP</span>, <span class='no'>TEC</span>, <span class='no'>TCY</span>, <span class='no'>ERY</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>pca_model</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='kw'>mo</span>) <span class='op'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(species = <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='kw'>mo</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='kw'>is.rsi</span>, <span class='kw'>resistance</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='pca.html'>pca</a></span>(<span class='kw'>FLC</span>, <span class='kw'>AMC</span>, <span class='kw'>CXM</span>, <span class='kw'>GEN</span>, <span class='kw'>TOB</span>, <span class='kw'>TMP</span>, <span class='kw'>SXT</span>, <span class='kw'>CIP</span>, <span class='kw'>TEC</span>, <span class='kw'>TCY</span>, <span class='kw'>ERY</span>)
<span class='co'># old (base R)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_model</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='kw'>pca_model</span>)
<span class='co'># new </span>
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>)) {
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span>() +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Title here"</span>)
<span class='fu'>ggplot_pca</span>(<span class='kw'>pca_model</span>)
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>)) {
<span class='fu'>ggplot_pca</span>(<span class='kw'>pca_model</span>) <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span>() <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(title = <span class='st'>"Title here"</span>)
}
}</pre>
</div>
@@ -423,7 +423,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

200
docs/reference/ggplot_rsi.html
View File

@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>AMR plots with <code>ggplot2</code> — ggplot_rsi • AMR (for R)</title>
<title>AMR plots with ggplot2 — ggplot_rsi • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
<meta property="og:title" content="AMR plots with ggplot2 — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on ggplot2 functions." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,61 +236,61 @@
</div>
<pre class="usage"><span class='fu'>ggplot_rsi</span>(
<span class='no'>data</span>,
<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
<span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span> <span class='st'>"#61f7ff"</span>, <span class='kw'>IR</span> <span class='kw'>=</span> <span class='st'>"#ff6961"</span>, <span class='kw'>R</span> <span class='kw'>=</span>
<span class='kw'>data</span>,
position = <span class='kw'>NULL</span>,
x = <span class='st'>"antibiotic"</span>,
fill = <span class='st'>"interpretation"</span>,
facet = <span class='kw'>NULL</span>,
breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
limits = <span class='kw'>NULL</span>,
translate_ab = <span class='st'>"name"</span>,
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
nrow = <span class='kw'>NULL</span>,
colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(S = <span class='st'>"#61a8ff"</span>, SI = <span class='st'>"#61a8ff"</span>, I = <span class='st'>"#61f7ff"</span>, IR = <span class='st'>"#ff6961"</span>, R =
<span class='st'>"#ff6961"</span>),
<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>2.5</span>,
<span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>,
<span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antimicrobial"</span>,
<span class='kw'>y.title</span> <span class='kw'>=</span> <span class='st'>"Proportion"</span>,
<span class='no'>...</span>
datalabels = <span class='fl'>TRUE</span>,
datalabels.size = <span class='fl'>2.5</span>,
datalabels.colour = <span class='st'>"gray15"</span>,
title = <span class='kw'>NULL</span>,
subtitle = <span class='kw'>NULL</span>,
caption = <span class='kw'>NULL</span>,
x.title = <span class='st'>"Antimicrobial"</span>,
y.title = <span class='st'>"Proportion"</span>,
<span class='kw'>...</span>
)
<span class='fu'>geom_rsi</span>(
<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
position = <span class='kw'>NULL</span>,
x = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
fill = <span class='st'>"interpretation"</span>,
translate_ab = <span class='st'>"name"</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>facet_rsi</span>(facet = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span>), nrow = <span class='kw'>NULL</span>)
<span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>scale_y_percent</span>(breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), limits = <span class='kw'>NULL</span>)
<span class='fu'>scale_rsi_colours</span>(
<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span> <span class='st'>"#61f7ff"</span>, <span class='kw'>IR</span> <span class='kw'>=</span> <span class='st'>"#ff6961"</span>, <span class='kw'>R</span> <span class='kw'>=</span>
colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(S = <span class='st'>"#61a8ff"</span>, SI = <span class='st'>"#61a8ff"</span>, I = <span class='st'>"#61f7ff"</span>, IR = <span class='st'>"#ff6961"</span>, R =
<span class='st'>"#ff6961"</span>)
)
<span class='fu'>theme_rsi</span>()
<span class='fu'>labels_rsi_count</span>(
<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>
position = <span class='kw'>NULL</span>,
x = <span class='st'>"antibiotic"</span>,
translate_ab = <span class='st'>"name"</span>,
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>,
datalabels.size = <span class='fl'>3</span>,
datalabels.colour = <span class='st'>"gray15"</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -412,79 +412,79 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>) <span class='op'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>)) <span class='op'>+</span>
<span class='fu'>geom_rsi</span>()
<span class='co'># prettify the plot using some additional functions:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
<span class='fu'>geom_rsi</span>() +
<span class='fu'>scale_y_percent</span>() +
<span class='fu'>scale_rsi_colours</span>() +
<span class='fu'>labels_rsi_count</span>() +
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>)
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>df</span>) <span class='op'>+</span>
<span class='fu'>geom_rsi</span>() <span class='op'>+</span>
<span class='fu'>scale_y_percent</span>() <span class='op'>+</span>
<span class='fu'>scale_rsi_colours</span>() <span class='op'>+</span>
<span class='fu'>labels_rsi_count</span>() <span class='op'>+</span>
<span class='fu'>theme_rsi</span>()
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>()
<span class='co'># get only proportions and no counts:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(datalabels = <span class='fl'>FALSE</span>)
<span class='co'># add other ggplot2 parameters as you like:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
<span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>linetype</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"yellow"</span>))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(width = <span class='fl'>0.5</span>,
colour = <span class='st'>"black"</span>,
size = <span class='fl'>1</span>,
linetype = <span class='fl'>2</span>,
alpha = <span class='fl'>0.25</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(SI = <span class='st'>"yellow"</span>))
}
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(first_isolate = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>first_isolate</span> <span class='op'>==</span> <span class='fl'>TRUE</span>,
<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%&gt;%</span>
<span class='co'># `age_group` is also a function of this package:</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(age_group = <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='kw'>age</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>age_group</span>,
<span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(x = <span class='st'>"age_group"</span>)
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() <span class='op'>+</span> <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='co'># a shorter version which also adjusts data label colours:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(colours = <span class='fl'>FALSE</span>)
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"hospital_id"</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>,
<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(x = <span class='st'>"hospital_id"</span>,
facet = <span class='st'>"antibiotic"</span>,
nrow = <span class='fl'>1</span>,
title = <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
x.title = <span class='st'>"Hospital"</span>,
datalabels = <span class='fl'>FALSE</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -501,7 +501,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

32
docs/reference/guess_ab_col.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>This tries to find a column name in a data set based on information from the <a href='antibiotics.html'>antibiotics</a> data set. Also supports WHONET abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>guess_ab_col</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>search_string</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<pre class="usage"><span class='fu'>guess_ab_col</span>(x = <span class='kw'>NULL</span>, search_string = <span class='kw'>NULL</span>, verbose = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -273,32 +273,32 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"S"</span>,
<span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"R"</span>)
<pre class="examples"><span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(amox = <span class='st'>"S"</span>,
tetr = <span class='st'>"R"</span>)
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"amoxicillin"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"amoxicillin"</span>)
<span class='co'># [1] "amox"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of tetracycline</span>
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of tetracycline</span>
<span class='co'># [1] "tetr"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>, verbose = <span class='fl'>TRUE</span>)
<span class='co'># NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).</span>
<span class='co'># [1] "tetr"</span>
<span class='co'># WHONET codes</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>AMP_ND10</span> <span class='kw'>=</span> <span class='st'>"R"</span>,
<span class='kw'>AMC_ED20</span> <span class='kw'>=</span> <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ND10 = <span class='st'>"R"</span>,
AMC_ED20 = <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='co'># [1] "AMP_ND10"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01CR02"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01CR02"</span>)
<span class='co'># [1] "AMC_ED20"</span>
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"augmentin"</span>))
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"augmentin"</span>))
<span class='co'># [1] "AMC_ED20"</span>
<span class='co'># Longer names take precendence:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>AMP_ED2</span> <span class='kw'>=</span> <span class='st'>"S"</span>,
<span class='kw'>AMP_ED20</span> <span class='kw'>=</span> <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ED2 = <span class='st'>"S"</span>,
AMP_ED20 = <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
<span class='co'># [1] "AMP_ED20"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -315,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/reference/index.html
View File

@@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -633,7 +633,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

42
docs/reference/join.html
View File

@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Join <a href='microorganisms.html'>microorganisms</a> to a data set — join • AMR (for R)</title>
<title>Join microorganisms to a data set — join • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Join <a href='microorganisms.html'>microorganisms</a> to a data set — join" />
<meta property="og:title" content="Join microorganisms to a data set — join" />
<meta property="og:description" content="Join the data set microorganisms easily to an existing table or character vector." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,17 +235,17 @@
<p>Join the data set <a href='microorganisms.html'>microorganisms</a> easily to an existing table or character vector.</p>
</div>
<pre class="usage"><span class='fu'>inner_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<pre class="usage"><span class='fu'>inner_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<span class='fu'>left_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<span class='fu'>left_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<span class='fu'>right_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<span class='fu'>right_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<span class='fu'>full_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<span class='fu'>full_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
<span class='fu'>semi_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
<span class='fu'>semi_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, <span class='kw'>...</span>)
<span class='fu'>anti_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
<span class='fu'>anti_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, <span class='kw'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -289,19 +289,19 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))
<span class='fu'>left_join_microorganisms</span>(<span class='st'>"B_KLBSL_PNE"</span>)
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>left_join_microorganisms</span>()
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>left_join_microorganisms</span>()
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='kw'>from</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-01"</span>),
<span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-07"</span>),
<span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>1</span>),
<span class='kw'>bacteria</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S. aureus"</span>, <span class='st'>"MRSA"</span>, <span class='st'>"MSSA"</span>, <span class='st'>"STAAUR"</span>,
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(date = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(from = <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-01"</span>),
to = <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-07"</span>),
by = <span class='fl'>1</span>),
bacteria = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S. aureus"</span>, <span class='st'>"MRSA"</span>, <span class='st'>"MSSA"</span>, <span class='st'>"STAAUR"</span>,
<span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>)),
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='no'>df</span>)
<span class='no'>df_joined</span> <span class='kw'>&lt;-</span> <span class='fu'>left_join_microorganisms</span>(<span class='no'>df</span>, <span class='st'>"bacteria"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='no'>df_joined</span>)
stringsAsFactors = <span class='fl'>FALSE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='kw'>df</span>)
<span class='kw'>df_joined</span> <span class='op'>&lt;-</span> <span class='fu'>left_join_microorganisms</span>(<span class='kw'>df</span>, <span class='st'>"bacteria"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='kw'>df_joined</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

88
docs/reference/key_antibiotics.html
View File

@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Key antibiotics for first <em>weighted</em> isolates — key_antibiotics • AMR (for R)</title>
<title>Key antibiotics for first weighted isolates — key_antibiotics • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" />
<meta property="og:title" content="Key antibiotics for first weighted isolates — key_antibiotics" />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,37 +236,37 @@
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span>(
<span class='no'>x</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"amoxicillin"</span>),
<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span>),
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"cefuroxime"</span>),
<span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"piperacillin/tazobactam"</span>),
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ciprofloxacin"</span>),
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span>),
<span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"vancomycin"</span>),
<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"teicoplanin"</span>),
<span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tetracycline"</span>),
<span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"erythromycin"</span>),
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"oxacillin"</span>),
<span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"rifampin"</span>),
<span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"gentamicin"</span>),
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tobramycin"</span>),
<span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"colistin"</span>),
<span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"cefotaxime"</span>),
<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ceftazidime"</span>),
<span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"meropenem"</span>),
<span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_mo = <span class='kw'>NULL</span>,
universal_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"amoxicillin"</span>),
universal_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span>),
universal_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"cefuroxime"</span>),
universal_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"piperacillin/tazobactam"</span>),
universal_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"ciprofloxacin"</span>),
universal_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span>),
GramPos_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"vancomycin"</span>),
GramPos_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"teicoplanin"</span>),
GramPos_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"tetracycline"</span>),
GramPos_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"erythromycin"</span>),
GramPos_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"oxacillin"</span>),
GramPos_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"rifampin"</span>),
GramNeg_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"gentamicin"</span>),
GramNeg_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"tobramycin"</span>),
GramNeg_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"colistin"</span>),
GramNeg_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"cefotaxime"</span>),
GramNeg_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"ceftazidime"</span>),
GramNeg_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"meropenem"</span>),
warnings = <span class='fl'>TRUE</span>,
<span class='kw'>...</span>
)
<span class='fu'>key_antibiotics_equal</span>(
<span class='no'>y</span>,
<span class='no'>z</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
<span class='kw'>y</span>,
<span class='kw'>z</span>,
type = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
ignore_I = <span class='fl'>TRUE</span>,
points_threshold = <span class='fl'>2</span>,
info = <span class='fl'>FALSE</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -388,31 +388,31 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='kw'>my_patients</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(keyab = <span class='fu'>key_antibiotics</span>(<span class='kw'>.</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
<span class='co'># now calculate first isolates</span>
<span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
first_regular = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>, col_keyantibiotics = <span class='fl'>FALSE</span>),
<span class='co'># and first WEIGHTED isolates</span>
<span class='kw'>first_weighted</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>"keyab"</span>)
first_weighted = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>, col_keyantibiotics = <span class='st'>"keyab"</span>)
)
<span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='kw'>my_patients</span><span class='op'>$</span><span class='kw'>first_regular</span>, na.rm = <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='kw'>my_patients</span><span class='op'>$</span><span class='kw'>first_weighted</span>, na.rm = <span class='fl'>TRUE</span>)
}
<span class='co'># output of the `key_antibiotics` function could be like this:</span>
<span class='no'>strainA</span> <span class='kw'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>
<span class='no'>strainB</span> <span class='kw'>&lt;-</span> <span class='st'>"SSSIRSSSRSSS"</span>
<span class='kw'>strainA</span> <span class='op'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>
<span class='kw'>strainB</span> <span class='op'>&lt;-</span> <span class='st'>"SSSIRSSSRSSS"</span>
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='kw'>strainA</span>, <span class='kw'>strainB</span>)
<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='kw'>strainA</span>, <span class='kw'>strainB</span>, ignore_I = <span class='fl'>FALSE</span>)
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -429,7 +429,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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12
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@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,16 +235,16 @@
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.</p>
</div>
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for default</span>
<span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for matrix</span>
<span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for data.frame</span>
<span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -289,7 +289,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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8
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Lifecycles of functions in the <code>AMR</code> package — lifecycle • AMR (for R)</title>
<title>Lifecycles of functions in the AMR package — lifecycle • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Lifecycles of functions in the <code>AMR</code> package — lifecycle" />
<meta property="og:title" content="Lifecycles of functions in the AMR package — lifecycle" />
<meta property="og:description" content="Functions in this AMR package are categorised using the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle.
This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions." />
@@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -288,7 +288,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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32
docs/reference/like.html
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@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,11 +235,11 @@
<p>Convenient wrapper around <code><a href='https://rdrr.io/r/base/grep.html'>grep()</a></code> to match a pattern: <code>x %like% pattern</code>. It always returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector and is always case-insensitive (use <code>x %like_case% pattern</code> for case-sensitive matching). Also, <code>pattern</code> can be as long as <code>x</code> to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.</p>
</div>
<pre class="usage"><span class='fu'>like</span>(<span class='no'>x</span>, <span class='no'>pattern</span>, <span class='kw'>ignore.case</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<pre class="usage"><span class='fu'>like</span>(<span class='kw'>x</span>, <span class='kw'>pattern</span>, ignore.case = <span class='fl'>TRUE</span>)
<span class='no'>x</span> <span class='kw'>%like%</span> <span class='no'>pattern</span>
<span class='kw'>x</span> <span class='op'>%like%</span> <span class='kw'>pattern</span>
<span class='no'>x</span> <span class='kw'>%like_case%</span> <span class='no'>pattern</span></pre>
<span class='kw'>x</span> <span class='op'>%like_case%</span> <span class='kw'>pattern</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -292,24 +292,24 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># simple test</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='st'>"This is a test"</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='st'>"TEST"</span>
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='kw'>a</span> <span class='op'>&lt;-</span> <span class='st'>"This is a test"</span>
<span class='kw'>b</span> <span class='op'>&lt;-</span> <span class='st'>"TEST"</span>
<span class='kw'>a</span> <span class='op'>%like%</span> <span class='kw'>b</span>
<span class='co'>#&gt; TRUE</span>
<span class='no'>b</span> <span class='kw'>%like%</span> <span class='no'>a</span>
<span class='kw'>b</span> <span class='op'>%like%</span> <span class='kw'>a</span>
<span class='co'>#&gt; FALSE</span>
<span class='co'># also supports multiple patterns, length must be equal to x</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span>)
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( <span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='kw'>a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span>)
<span class='kw'>b</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( <span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
<span class='kw'>a</span> <span class='op'>%like%</span> <span class='kw'>b</span>
<span class='co'>#&gt; TRUE TRUE TRUE</span>
<span class='co'># get isolates whose name start with 'Ent' or 'ent'</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>"^ent"</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"^ent"</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -326,7 +326,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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50
docs/reference/mdro.html
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@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,25 +236,25 @@
</div>
<pre class="usage"><span class='fu'>mdro</span>(
<span class='no'>x</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CMI2012"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>pct_required_classes</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
guideline = <span class='st'>"CMI2012"</span>,
col_mo = <span class='kw'>NULL</span>,
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
pct_required_classes = <span class='fl'>0.5</span>,
combine_SI = <span class='fl'>TRUE</span>,
verbose = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='fu'>brmo</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"BRMO"</span>, <span class='no'>...</span>)
<span class='fu'>brmo</span>(<span class='kw'>x</span>, guideline = <span class='st'>"BRMO"</span>, <span class='kw'>...</span>)
<span class='fu'>mrgn</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"MRGN"</span>, <span class='no'>...</span>)
<span class='fu'>mrgn</span>(<span class='kw'>x</span>, guideline = <span class='st'>"MRGN"</span>, <span class='kw'>...</span>)
<span class='fu'>mdr_tb</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"TB"</span>, <span class='no'>...</span>)
<span class='fu'>mdr_tb</span>(<span class='kw'>x</span>, guideline = <span class='st'>"TB"</span>, <span class='kw'>...</span>)
<span class='fu'>mdr_cmi2012</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CMI2012"</span>, <span class='no'>...</span>)
<span class='fu'>mdr_cmi2012</span>(<span class='kw'>x</span>, guideline = <span class='st'>"CMI2012"</span>, <span class='kw'>...</span>)
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='kw'>x</span>, guideline = <span class='st'>"EUCAST"</span>, <span class='kw'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -440,18 +440,18 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>cleaner</span>)
<pre class="examples"><span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://github.com/msberends/cleaner'>cleaner</a></span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>mdro</span>() <span class='kw'>%&gt;%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>mdro</span>() <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>()
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>.</span>),
<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>),
<span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(EUCAST = <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='kw'>.</span>),
BRMO = <span class='fu'>brmo</span>(<span class='kw'>.</span>),
MRGN = <span class='fu'>mrgn</span>(<span class='kw'>.</span>))
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -468,7 +468,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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6
docs/reference/microorganisms.codes.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>. They will all be searched when using <code><a href='as.mo.html'>as.mo()</a></code> and consequently all the <code><a href='mo_property.html'>mo_*</a></code> functions.</p>
</div>
<pre class="usage"><span class='no'>microorganisms.codes</span></pre>
<pre class="usage"><span class='kw'>microorganisms.codes</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -276,7 +276,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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6
docs/reference/microorganisms.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using <code><a href='as.mo.html'>as.mo()</a></code>.</p>
</div>
<pre class="usage"><span class='no'>microorganisms</span></pre>
<pre class="usage"><span class='kw'>microorganisms</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -319,7 +319,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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6
docs/reference/microorganisms.old.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href='as.mo.html'>as.mo()</a></code>.</p>
</div>
<pre class="usage"><span class='no'>microorganisms.old</span></pre>
<pre class="usage"><span class='kw'>microorganisms.old</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -282,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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74
docs/reference/mo_property.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,53 +235,53 @@
<p>Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. Please see <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>mo_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<pre class="usage"><span class='fu'>mo_name</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_fullname</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_shortname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_shortname</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_subspecies</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_subspecies</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_species</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_species</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_genus</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_genus</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_family</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_family</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_order</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_order</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_class</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_class</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_phylum</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_phylum</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_kingdom</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_kingdom</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_domain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_domain</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_type</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_type</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_gramstain</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_snomed</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_snomed</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>mo_ref</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_ref</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>mo_authors</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_authors</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>mo_year</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_year</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>mo_rank</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_rank</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_taxonomy</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_synonyms</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_synonyms</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<span class='fu'>mo_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_info</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
<span class='fu'>mo_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>mo_url</span>(<span class='kw'>x</span>, open = <span class='fl'>FALSE</span>, <span class='kw'>...</span>)
<span class='fu'>mo_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"fullname"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
<span class='fu'>mo_property</span>(<span class='kw'>x</span>, property = <span class='st'>"fullname"</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -416,21 +416,21 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='co'># \donttest{</span>
<span class='co'># Becker classification, see ?as.mo ----------------------------------------</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "Staphylococcus epidermidis"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "S. epidermidis"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "CoNS"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># "CoNS"</span>
<span class='co'># Lancefield classification, see ?as.mo ------------------------------------</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "Streptococcus pyogenes"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Streptococcus group A"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># "Streptococcus group A"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "S. pyogenes"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "GAS" (='Group A Streptococci')</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># "GAS" (='Group A Streptococci')</span>
<span class='co'># language support for German, Dutch, Spanish, Portuguese, Italian and French</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>) <span class='co'># "Gramnegativ"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='co'># "Gram-negatief"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>) <span class='co'># "Gram negativo"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"de"</span>) <span class='co'># "Gramnegativ"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"nl"</span>) <span class='co'># "Gram-negatief"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"es"</span>) <span class='co'># "Gram negativo"</span>
<span class='co'># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on a German system</span>
@@ -438,11 +438,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on an English system</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>) <span class='co'># "Streptococcus Gruppe A"</span>
Lancefield = <span class='fl'>TRUE</span>,
language = <span class='st'>"de"</span>) <span class='co'># "Streptococcus Gruppe A"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='co'># "Streptococcus groep A"</span>
Lancefield = <span class='fl'>TRUE</span>,
language = <span class='st'>"nl"</span>) <span class='co'># "Streptococcus groep A"</span>
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
@@ -465,7 +465,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

24
docs/reference/mo_source.html
View File

@@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -237,7 +237,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
</div>
<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='no'>path</span>)
<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='kw'>path</span>)
<span class='fu'>get_mo_source</span>()</pre>
@@ -270,19 +270,19 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</pre>
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span>(<span class='st'>"home/me/ourcodes.xlsx"</span>)
<span class='co'>#&amp;gt; NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&amp;gt; (columns "Organisation XYZ" and "mo")</span></pre>
<span class='co'>#&gt; NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&gt; (columns "Organisation XYZ" and "mo")</span></pre>
<p>It has now created a file <code>"~/.mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
<p>And now we can use it in our functions:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
<span class='co'>#&amp;gt; [1] B_ESCHR_COLI</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_mo_kpneumoniae"</span>)
<span class='co'>#&amp;gt; [1] "Klebsiella"</span>
<span class='co'>#&gt; [1] "Klebsiella"</span>
<span class='co'># other input values still work too</span>
<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Escherichia coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"lab_mo_ecoli"</span>))
<span class='co'>#&amp;gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></pre>
<span class='co'>#&gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></pre>
<p>If we edit the Excel file by, let's say, adding row 4 like this:</p><pre> | A | B |
--|--------------------|--------------|
@@ -294,12 +294,12 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</pre>
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
<span class='co'>#&amp;gt; NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&amp;gt; (columns "Organisation XYZ" and "mo")</span>
<span class='co'>#&amp;gt; [1] B_ESCHR_COLI</span>
<span class='co'>#&gt; NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
<span class='co'>#&gt; (columns "Organisation XYZ" and "mo")</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_Staph_aureus"</span>)
<span class='co'>#&amp;gt; [1] "Staphylococcus"</span></pre>
<span class='co'>#&gt; [1] "Staphylococcus"</span></pre>
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre><span class='fu'>set_mo_source</span>(<span class='kw'>NULL</span>)
<span class='co'># Removed mo_source file '~/.mo_source.rds'.</span></pre>
@@ -333,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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8
docs/reference/p_symbol.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -232,10 +232,10 @@
</div>
<div class="ref-description">
<p>Return the symbol related to the p-value: 0 '<code>***</code>' 0.001 '<code>**</code>' 0.01 '<code>*</code>' 0.05 '<code>.</code>' 0.1 ' ' 1. Values above <code>p = 1</code> will return <code>NA</code>.</p>
<p>Return the symbol related to the p-value: 0 '<code>***</code>' 0.001 '<code>**</code>' 0.01 '<code><a href='https://rdrr.io/r/base/Arithmetic.html'>*</a></code>' 0.05 '<code>.</code>' 0.1 ' ' 1. Values above <code>p = 1</code> will return <code>NA</code>.</p>
</div>
<pre class="usage"><span class='fu'>p_symbol</span>(<span class='no'>p</span>, <span class='kw'>emptychar</span> <span class='kw'>=</span> <span class='st'>" "</span>)</pre>
<pre class="usage"><span class='fu'>p_symbol</span>(<span class='kw'>p</span>, emptychar = <span class='st'>" "</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -280,7 +280,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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46
docs/reference/pca.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,13 +236,13 @@
</div>
<pre class="usage"><span class='fu'>pca</span>(
<span class='no'>x</span>,
<span class='no'>...</span>,
<span class='kw'>retx</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>center</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>scale.</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>tol</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>rank.</span> <span class='kw'>=</span> <span class='kw'>NULL</span>
<span class='kw'>x</span>,
<span class='kw'>...</span>,
retx = <span class='fl'>TRUE</span>,
center = <span class='fl'>TRUE</span>,
scale. = <span class='fl'>TRUE</span>,
tol = <span class='kw'>NULL</span>,
rank. = <span class='kw'>NULL</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -315,22 +315,22 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># calculate the resistance per group first</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>resistance_data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>order</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_order</a></span>(<span class='no'>mo</span>), <span class='co'># group on anything, like order</span>
<span class='kw'>genus</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>)) <span class='kw'>%&gt;%</span> <span class='co'># and genus as we do here</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span>(<span class='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='co'># then get resistance of all drugs</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>resistance_data</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(order = <span class='fu'><a href='mo_property.html'>mo_order</a></span>(<span class='kw'>mo</span>), <span class='co'># group on anything, like order</span>
genus = <span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='kw'>mo</span>)) <span class='op'>%&gt;%</span> <span class='co'># and genus as we do here</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span>(<span class='kw'>is.rsi</span>, <span class='kw'>resistance</span>) <span class='co'># then get resistance of all drugs</span>
<span class='co'># now conduct PCA for certain antimicrobial agents</span>
<span class='no'>pca_result</span> <span class='kw'>&lt;-</span> <span class='no'>resistance_data</span> <span class='kw'>%&gt;%</span>
<span class='fu'>pca</span>(<span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>CTX</span>, <span class='no'>CAZ</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>)
<span class='no'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>pca_result</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_result</span>)
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='no'>pca_result</span>) <span class='co'># a new and convenient plot function</span>
<span class='kw'>pca_result</span> <span class='op'>&lt;-</span> <span class='kw'>resistance_data</span> <span class='op'>%&gt;%</span>
<span class='fu'>pca</span>(<span class='kw'>AMC</span>, <span class='kw'>CXM</span>, <span class='kw'>CTX</span>, <span class='kw'>CAZ</span>, <span class='kw'>GEN</span>, <span class='kw'>TOB</span>, <span class='kw'>TMP</span>, <span class='kw'>SXT</span>)
<span class='kw'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>pca_result</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='kw'>pca_result</span>)
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='kw'>pca_result</span>) <span class='co'># a new and convenient plot function</span>
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -347,7 +347,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

199
docs/reference/proportion.html
View File

@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -233,42 +233,42 @@ resistance() should be used to calculate resistance, susceptibility() should be
</div>
<div class="ref-description">
<p>These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>summarise()</code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
<p>These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
</div>
<pre class="usage"><span class='fu'>resistance</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>resistance</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>susceptibility</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>susceptibility</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>proportion_R</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_R</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>proportion_IR</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_IR</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>proportion_I</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_I</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>proportion_SI</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_SI</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>proportion_S</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_S</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>proportion_df</span>(
<span class='no'>data</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
<span class='kw'>data</span>,
translate_ab = <span class='st'>"name"</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
minimum = <span class='fl'>30</span>,
as_percent = <span class='fl'>FALSE</span>,
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>
)
<span class='fu'>rsi_df</span>(
<span class='no'>data</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
<span class='kw'>data</span>,
translate_ab = <span class='st'>"name"</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
minimum = <span class='fl'>30</span>,
as_percent = <span class='fl'>FALSE</span>,
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -336,22 +336,21 @@ resistance() should be used to calculate resistance, susceptibility() should be
-------- -------- ---------- ----------- ---------- -----------
S or I S or I X X X X
R S or I X X X X
&amp;lt;NA&amp;gt; S or I X X - -
&lt;NA&gt; S or I X X - -
S or I R X X X X
R R - X - X
&amp;lt;NA&amp;gt; R - - - -
S or I &amp;lt;NA&amp;gt; X X - -
R &amp;lt;NA&amp;gt; - - - -
&amp;lt;NA&amp;gt; &amp;lt;NA&amp;gt; - - - -
&lt;NA&gt; R - - - -
S or I &lt;NA&gt; X X - -
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() + <span class='fu'><a href='count.html'>count_I</a></span>() + <span class='fu'><a href='count.html'>count_R</a></span>() <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
<span class='fu'>proportion_S</span>() + <span class='fu'>proportion_I</span>() + <span class='fu'>proportion_R</span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>=</span> <span class='fl'>1</span></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &amp;gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &amp;gt;= 1
</pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>&gt;=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>&gt;=</span> <span class='fl'>1</span></pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@@ -386,84 +385,84 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
?<span class='no'>example_isolates</span>
<span class='op'>?</span><span class='kw'>example_isolates</span>
<span class='fu'>resistance</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># determines %R</span>
<span class='fu'>susceptibility</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># determines %S+I</span>
<span class='fu'>resistance</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %R</span>
<span class='fu'>susceptibility</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %S+I</span>
<span class='co'># be more specific</span>
<span class='fu'>proportion_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_I</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>r</span> <span class='kw'>=</span> <span class='fu'>resistance</span>(<span class='no'>CIP</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>resistance</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>SI</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='fu'>proportion_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>proportion_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>proportion_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>proportion_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>proportion_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(r = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>),
n = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(R = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
SI = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
n1 = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
n2 = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
total = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>) <span class='co'># %SI = 76.3%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='no'>GEN</span>) <span class='co'># %SI = 75.4%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># %SI = 94.1%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># n = 1939</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>) <span class='co'># %SI = 76.3%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>) <span class='co'># n = 1879</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>) <span class='co'># %SI = 75.4%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>) <span class='co'># n = 1855</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># %SI = 94.1%</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># n = 1939</span>
<span class='co'># See Details on how `only_all_tested` works. Example:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
<span class='kw'>proportion</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>proportion</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>),
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>),
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>))
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(cipro_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
cipro_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>),
genta_p = <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
genta_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>),
combination_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
combination_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>))
<span class='co'># Get proportions S/I/R immediately of all rsi columns</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>proportion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>proportion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
}
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
<span class='no'>my_table</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>), <span class='co'># amoxicillin with metronidazole</span>
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>))
<span class='kw'>my_table</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>first_isolate</span> <span class='op'>==</span> <span class='fl'>TRUE</span>,
<span class='kw'>genus</span> <span class='op'>==</span> <span class='st'>"Helicobacter"</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(p = <span class='fu'>susceptibility</span>(<span class='kw'>AMX</span>, <span class='kw'>MTR</span>), <span class='co'># amoxicillin with metronidazole</span>
n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMX</span>, <span class='kw'>MTR</span>))
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -480,7 +479,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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140
docs/reference/resistance_predict.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,43 +236,43 @@
</div>
<pre class="usage"><span class='fu'>resistance_predict</span>(
<span class='no'>x</span>,
<span class='no'>col_ab</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>year_min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>year_max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>year_every</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='no'>...</span>
<span class='kw'>x</span>,
<span class='kw'>col_ab</span>,
col_date = <span class='kw'>NULL</span>,
year_min = <span class='kw'>NULL</span>,
year_max = <span class='kw'>NULL</span>,
year_every = <span class='fl'>1</span>,
minimum = <span class='fl'>30</span>,
model = <span class='kw'>NULL</span>,
I_as_S = <span class='fl'>TRUE</span>,
preserve_measurements = <span class='fl'>TRUE</span>,
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>...</span>
)
<span class='fu'>rsi_predict</span>(
<span class='no'>x</span>,
<span class='no'>col_ab</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>year_min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>year_max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>year_every</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='no'>...</span>
<span class='kw'>x</span>,
<span class='kw'>col_ab</span>,
col_date = <span class='kw'>NULL</span>,
year_min = <span class='kw'>NULL</span>,
year_max = <span class='kw'>NULL</span>,
year_every = <span class='fl'>1</span>,
minimum = <span class='fl'>30</span>,
model = <span class='kw'>NULL</span>,
I_as_S = <span class='fl'>TRUE</span>,
preserve_measurements = <span class='fl'>TRUE</span>,
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>...</span>
)
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='no'>x_name</span>), <span class='no'>...</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>x</span>, main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='kw'>x_name</span>), <span class='kw'>...</span>)
<span class='fu'>ggplot_rsi_predict</span>(
<span class='no'>x</span>,
<span class='kw'>main</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='no'>x_name</span>),
<span class='kw'>ribbon</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='kw'>x_name</span>),
ribbon = <span class='fl'>TRUE</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -388,56 +388,56 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p>Models: <code><a href='https://rdrr.io/r/stats/lm.html'>lm()</a></code> <code><a href='https://rdrr.io/r/stats/glm.html'>glm()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>resistance_predict</span>(<span class='no'>example_isolates</span>,
<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>)) {
<span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
<pre class="examples"><span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='fu'>resistance_predict</span>(<span class='kw'>example_isolates</span>,
col_ab = <span class='st'>"AMX"</span>,
year_min = <span class='fl'>2010</span>,
model = <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>x</span>)
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>)) {
<span class='fu'>ggplot_rsi_predict</span>(<span class='kw'>x</span>)
}
<span class='co'># using dplyr:</span>
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='kw'>x</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='kw'>mo</span>) <span class='op'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='op'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, model = <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>x</span>)
<span class='co'># get the model from the object</span>
<span class='no'>mymodel</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='no'>x</span>)$<span class='no'>model</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>mymodel</span>)
<span class='kw'>mymodel</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='kw'>x</span>)<span class='op'>$</span><span class='kw'>model</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>mymodel</span>)
}
<span class='co'># create nice plots with ggplot2 yourself</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>ggplot2</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='http://ggplot2.tidyverse.org'>ggplot2</a></span>)
<span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>15</span>)
<span class='kw'>data</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(col_ab = <span class='st'>"AMX"</span>,
col_date = <span class='st'>"date"</span>,
model = <span class='st'>"binomial"</span>,
info = <span class='fl'>FALSE</span>,
minimum = <span class='fl'>15</span>)
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>data</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>year</span>)) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>value</span>),
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"grey75"</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>ymin</span> <span class='kw'>=</span> <span class='no'>se_min</span>,
<span class='kw'>ymax</span> <span class='kw'>=</span> <span class='no'>se_max</span>),
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"grey50"</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span>(<span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
<span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span>), <span class='st'>"%"</span>)) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Forecast of Amoxicillin Resistance in "</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>data</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(x = <span class='kw'>year</span>)) <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(y = <span class='kw'>value</span>),
fill = <span class='st'>"grey75"</span>) <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(ymin = <span class='kw'>se_min</span>,
ymax = <span class='kw'>se_max</span>),
colour = <span class='st'>"grey50"</span>) <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span>(limits = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
labels = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span>), <span class='st'>"%"</span>)) <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(title = <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Forecast of Amoxicillin Resistance in "</span>,
<span class='fu'><a href='https://rdrr.io/r/grDevices/plotmath.html'>italic</a></span>(<span class='st'>"E. coli"</span>))),
<span class='kw'>y</span> <span class='kw'>=</span> <span class='st'>"%R"</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Year"</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
y = <span class='st'>"%R"</span>,
x = <span class='st'>"Year"</span>) <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(base_size = <span class='fl'>13</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -454,7 +454,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

6
docs/reference/rsi_translation.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -235,7 +235,7 @@
<p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<pre class="usage"><span class='no'>rsi_translation</span></pre>
<pre class="usage"><span class='kw'>rsi_translation</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -277,7 +277,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

12
docs/reference/skewness.html
View File

@@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -237,16 +237,16 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<p>When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.</p>
</div>
<pre class="usage"><span class='fu'>skewness</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for default</span>
<span class='fu'>skewness</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for matrix</span>
<span class='fu'>skewness</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for data.frame</span>
<span class='fu'>skewness</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -291,7 +291,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

16
docs/reference/translate.html
View File

@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -264,27 +264,27 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># with get_locale()</span>
<span class='co'># English</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"en"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"en"</span>)
<span class='co'>#&gt; "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class='co'># German</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"de"</span>)
<span class='co'>#&gt; "Koagulase-negative Staphylococcus (KNS)"</span>
<span class='co'># Dutch</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"nl"</span>)
<span class='co'>#&gt; "Coagulase-negatieve Staphylococcus (CNS)"</span>
<span class='co'># Spanish</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"es"</span>)
<span class='co'>#&gt; "Staphylococcus coagulasa negativo (SCN)"</span>
<span class='co'># Italian</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"it"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"it"</span>)
<span class='co'>#&gt; "Staphylococcus negativo coagulasi (CoNS)"</span>
<span class='co'># Portuguese</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"pt"</span>)
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"pt"</span>)
<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -301,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

4
docs/survey.html
View File

@@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -248,7 +248,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>

2
index.md
View File

@@ -4,7 +4,7 @@
> <span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> **PLEASE TAKE PART IN OUR SURVEY!**
> Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. **If you have a minute, please [anonymously fill in this short questionnaire](./survey.html)**. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!
> <br>
> <a class="btn btn-info btn-amr">Take me to the 5-min survey!</a>
> <a class="btn btn-info btn-amr" href="./survey.html">Take me to the 5-min survey!</a>
### What is `AMR` (for R)?

1
man/as.rsi.Rd
View File

@@ -162,6 +162,7 @@ as.rsi(df)
library(dplyr)
df \%>\% mutate_at(vars(AMP:TOB), as.rsi)
df \%>\% mutate(across(AMP:TOB), as.rsi)
df \%>\%
mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")

2
vignettes/welcome_to_AMR.Rmd
View File

@@ -24,6 +24,8 @@ knitr::opts_chunk$set(
)
```
**READ ALL VIGNETTES [ON OUR WEBSITE](https://msberends.github.io/AMR/articles/)**
# Welcome to the AMR package
`AMR` is a free, open-source and independent R package 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. **Our aim is to provide a standard** for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.