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atc_ functions
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@ -47,7 +47,7 @@
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<script src="../extra.js"></script>
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<meta property="og:title" content="Deprecated functions — AMR-deprecated" />
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<meta property="og:description" content="These functions are Deprecated. 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 Using the functions will give a warning with the name of the function it has been replaced by." />
|
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<meta property="og:description" content="These functions are so-called 'Deprecated'. 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 Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary" />
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@ -223,13 +223,29 @@
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<div class="ref-description">
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<p>These functions are <a href='https://www.rdocumentation.org/packages/base/topics/Deprecated'>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 Using the functions will give a warning with the name of the function it has been replaced by.</p>
|
||||
<p>These functions are so-called '<a href='https://www.rdocumentation.org/packages/base/topics/Deprecated'>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 Using the functions will give a warning with the name of the function it has been replaced by (if there is one).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>
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|
||||
</div>
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<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)
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<span class='fu'>guess_mo</span>(<span class='no'>...</span>)</pre>
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<span class='fu'>guess_mo</span>(<span class='no'>...</span>)
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<span class='fu'>ab_property</span>(<span class='no'>...</span>)
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<span class='fu'>ab_atc</span>(<span class='no'>...</span>)
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<span class='fu'>ab_official</span>(<span class='no'>...</span>)
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<span class='fu'>ab_name</span>(<span class='no'>...</span>)
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<span class='fu'>ab_trivial_nl</span>(<span class='no'>...</span>)
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<span class='fu'>ab_certe</span>(<span class='no'>...</span>)
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<span class='fu'>ab_umcg</span>(<span class='no'>...</span>)
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<span class='fu'>ab_tradenames</span>(<span class='no'>...</span>)</pre>
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<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>
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||||
|
@ -231,7 +231,7 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.</p>
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<p>This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).</p>
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<p>This package was created for both academic research and routine analysis by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).</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>
|
||||
|
||||
|
@ -246,9 +246,9 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='fu'><a href='as.atc.html'>as.atc</a></span>(<span class='st'>"meropenem"</span>)
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<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01DH02"</span>)
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<span class='fu'><a href='AMR-deprecated.html'>ab_name</a></span>(<span class='st'>"J01DH02"</span>)
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<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)
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<span class='fu'><a href='AMR-deprecated.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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|
@ -257,7 +257,7 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p><strong>The <code><a href='ab_property.html'>ab_property</a></code> functions are faster and more concise</strong>, but do not support concatenated strings, like <code>abname("AMCL+GENT"</code>.</p>
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<p><strong>The <code><a href='AMR-deprecated.html'>ab_property</a></code> functions are faster and more concise</strong>, but do not support concatenated strings, like <code>abname("AMCL+GENT"</code>.</p>
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<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
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|
@ -296,11 +296,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># resistance of ciprofloxacine per age group</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
|
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<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'>%>%</span>
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<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>,
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<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'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>age_group</span>,
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<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'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
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<span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<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>)
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<span class='co'># }</span></pre>
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@ -248,7 +248,7 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>Use the <code><a href='ab_property.html'>ab_property</a></code> functions to get properties based on the returned ATC code, see Examples.</p>
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<p>Use the <code><a href='AMR-deprecated.html'>ab_property</a></code> functions to get properties based on the returned ATC code, see Examples.</p>
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<p>In the ATC classification system, the active substances are classified in a hierarchy with five different levels. The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups. The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
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Source: <a href='https://www.whocc.no/atc/structure_and_principles/'>https://www.whocc.no/atc/structure_and_principles/</a></p>
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@ -286,8 +286,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># Use ab_* functions to get a specific property based on an ATC code</span>
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<span class='no'>Cipro</span> <span class='kw'><-</span> <span class='fu'>as.atc</span>(<span class='st'>"cipro"</span>) <span class='co'># returns `J01MA02`</span>
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<span class='fu'><a href='ab_property.html'>ab_official</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "Ciprofloxacin"</span>
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<span class='fu'><a href='ab_property.html'>ab_umcg</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "CIPR", the code used in the UMCG</span>
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<span class='fu'><a href='AMR-deprecated.html'>ab_official</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "Ciprofloxacin"</span>
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<span class='fu'><a href='AMR-deprecated.html'>ab_umcg</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "CIPR", the code used in the UMCG</span>
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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|
@ -277,11 +277,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># using dplyr's mutate</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise_all'>mutate_at</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/vars'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
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<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise_all'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
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<span class='no'>as.rsi</span>)
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<span class='co'># }</span></pre>
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</div>
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353
docs/reference/atc_online.html
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353
docs/reference/atc_online.html
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<h1>Properties of an ATC code</h1>
|
||||
|
||||
<div class="hidden name"><code>atc_online.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. <br /> <strong>This function requires an internet connection.</strong></p>
|
||||
|
||||
</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&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_ddd</span>(<span class='no'>atc_code</span>, <span class='no'>...</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>atc_code</th>
|
||||
<td><p>a character or character vector with ATC code(s) of antibiotic(s)</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
<td><p>property of an ATC code. Valid values are <code>"ATC"</code>, <code>"Name"</code>, <code>"DDD"</code>, <code>"U"</code> (<code>"unit"</code>), <code>"Adm.R"</code>, <code>"Note"</code> and <code>groups</code>. For this last option, all hierarchical groups of an ATC code will be returned, see Examples.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>administration</th>
|
||||
<td><p>type of administration when using <code>property = "Adm.R"</code>, see Details</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>url</th>
|
||||
<td><p>url of website of the WHO. The sign <code>%s</code> can be used as a placeholder for ATC codes.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>parameters to pass on to <code>atc_property</code></p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p><a href='https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/'>https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/</a></p>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Options for parameter <code>administration</code>:</p><ul>
|
||||
<li><p><code>"Implant"</code> = Implant</p></li>
|
||||
<li><p><code>"Inhal"</code> = Inhalation</p></li>
|
||||
<li><p><code>"Instill"</code> = Instillation</p></li>
|
||||
<li><p><code>"N"</code> = nasal</p></li>
|
||||
<li><p><code>"O"</code> = oral</p></li>
|
||||
<li><p><code>"P"</code> = parenteral</p></li>
|
||||
<li><p><code>"R"</code> = rectal</p></li>
|
||||
<li><p><code>"SL"</code> = sublingual/buccal</p></li>
|
||||
<li><p><code>"TD"</code> = transdermal</p></li>
|
||||
<li><p><code>"V"</code> = vaginal</p></li>
|
||||
</ul>
|
||||
<p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul>
|
||||
<li><p><code>"g"</code> = gram</p></li>
|
||||
<li><p><code>"mg"</code> = milligram</p></li>
|
||||
<li><p><code>"mcg"</code> = microgram</p></li>
|
||||
<li><p><code>"U"</code> = unit</p></li>
|
||||
<li><p><code>"TU"</code> = thousand units</p></li>
|
||||
<li><p><code>"MU"</code> = million units</p></li>
|
||||
<li><p><code>"mmol"</code> = millimole</p></li>
|
||||
<li><p><code>"ml"</code> = milliliter (e.g. eyedrops)</p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</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='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>
|
||||
<span class='co'># [4] "Penicillins with extended spectrum"</span>
|
||||
<span class='co'># }</span></pre>
|
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
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<title>Property of an antibiotic — atc_property • AMR (for R)</title>
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<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set, based on their ATC code. Get such a code with as.atc." />
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<div class="page-header">
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<h1>Properties of an ATC code</h1>
|
||||
<h1>Property of an antibiotic</h1>
|
||||
|
||||
<div class="hidden name"><code>atc_property.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. <br /> <strong>This function requires an internet connection.</strong></p>
|
||||
<p>Use these functions to return a specific property of an antibiotic from the <code><a href='antibiotics.html'>antibiotics</a></code> data set, based on their ATC code. Get such a code with <code><a href='as.atc.html'>as.atc</a></code>.</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>atc_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&showdescription=no"</span>)
|
||||
<pre class="usage"><span class='fu'>atc_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"official"</span>)
|
||||
|
||||
<span class='fu'>atc_groups</span>(<span class='no'>atc_code</span>, <span class='no'>...</span>)
|
||||
<span class='fu'>atc_official</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
|
||||
|
||||
<span class='fu'>atc_ddd</span>(<span class='no'>atc_code</span>, <span class='no'>...</span>)</pre>
|
||||
<span class='fu'>atc_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
|
||||
|
||||
<span class='fu'>atc_trivial_nl</span>(<span class='no'>x</span>)
|
||||
|
||||
<span class='fu'>atc_certe</span>(<span class='no'>x</span>)
|
||||
|
||||
<span class='fu'>atc_umcg</span>(<span class='no'>x</span>)
|
||||
|
||||
<span class='fu'>atc_tradenames</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>atc_code</th>
|
||||
<td><p>a character or character vector with ATC code(s) of antibiotic(s)</p></td>
|
||||
<th>x</th>
|
||||
<td><p>a (vector of a) valid <code><a href='as.atc.html'>atc</a></code> code or any text that can be coerced to a valid atc with <code><a href='as.atc.html'>as.atc</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
<td><p>property of an ATC code. Valid values are <code>"ATC"</code>, <code>"Name"</code>, <code>"DDD"</code>, <code>"U"</code> (<code>"unit"</code>), <code>"Adm.R"</code>, <code>"Note"</code> and <code>groups</code>. For this last option, all hierarchical groups of an ATC code will be returned, see Examples.</p></td>
|
||||
<td><p>one of the column names of one of the <code><a href='antibiotics.html'>antibiotics</a></code> data set, like <code>"atc"</code> and <code>"official"</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>administration</th>
|
||||
<td><p>type of administration when using <code>property = "Adm.R"</code>, see Details</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>url</th>
|
||||
<td><p>url of website of the WHO. The sign <code>%s</code> can be used as a placeholder for ATC codes.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>parameters to pass on to <code>atc_property</code></p></td>
|
||||
<th>language</th>
|
||||
<td><p>language of the returned text, defaults to English (<code>"en"</code>) and can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Either one of <code>"en"</code> (English) or <code>"nl"</code> (Dutch).</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p><a href='https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/'>https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/</a></p>
|
||||
<p>A vector of values. In case of <code>atc_tradenames</code>, if <code>x</code> is of length one, a vector will be returned. Otherwise a <code><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></code>, with <code>x</code> as names.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
<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>
|
||||
|
||||
<p>Options for parameter <code>administration</code>:</p><ul>
|
||||
<li><p><code>"Implant"</code> = Implant</p></li>
|
||||
<li><p><code>"Inhal"</code> = Inhalation</p></li>
|
||||
<li><p><code>"Instill"</code> = Instillation</p></li>
|
||||
<li><p><code>"N"</code> = nasal</p></li>
|
||||
<li><p><code>"O"</code> = oral</p></li>
|
||||
<li><p><code>"P"</code> = parenteral</p></li>
|
||||
<li><p><code>"R"</code> = rectal</p></li>
|
||||
<li><p><code>"SL"</code> = sublingual/buccal</p></li>
|
||||
<li><p><code>"TD"</code> = transdermal</p></li>
|
||||
<li><p><code>"V"</code> = vaginal</p></li>
|
||||
</ul>
|
||||
<p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul>
|
||||
<li><p><code>"g"</code> = gram</p></li>
|
||||
<li><p><code>"mg"</code> = milligram</p></li>
|
||||
<li><p><code>"mcg"</code> = microgram</p></li>
|
||||
<li><p><code>"U"</code> = unit</p></li>
|
||||
<li><p><code>"TU"</code> = thousand units</p></li>
|
||||
<li><p><code>"MU"</code> = million units</p></li>
|
||||
<li><p><code>"mmol"</code> = millimole</p></li>
|
||||
<li><p><code>"ml"</code> = milliliter (e.g. eyedrops)</p></li>
|
||||
</ul>
|
||||
|
||||
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
|
||||
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='antibiotics.html'>antibiotics</a></code></p></div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># What's the ATC of amoxicillin?</span>
|
||||
<span class='fu'><a href='as.atc.html'>guess_atc</a></span>(<span class='st'>"Amoxicillin"</span>)
|
||||
<span class='co'># [1] "J01CA04"</span>
|
||||
|
||||
<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
|
||||
<span class='fu'>atc_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_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span>)
|
||||
|
||||
<span class='fu'>atc_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='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>
|
||||
<span class='co'># [4] "Penicillins with extended spectrum"</span>
|
||||
<span class='fu'><a href='as.atc.html'>as.atc</a></span>(<span class='st'>"amcl"</span>) <span class='co'># J01CR02</span>
|
||||
<span class='fu'>atc_name</span>(<span class='st'>"amcl"</span>) <span class='co'># Amoxicillin and beta-lactamase inhibitor</span>
|
||||
<span class='fu'>atc_name</span>(<span class='st'>"amcl"</span>, <span class='st'>"nl"</span>) <span class='co'># Amoxicilline met enzymremmer</span>
|
||||
<span class='fu'>atc_trivial_nl</span>(<span class='st'>"amcl"</span>) <span class='co'># Amoxicilline/clavulaanzuur</span>
|
||||
<span class='fu'>atc_certe</span>(<span class='st'>"amcl"</span>) <span class='co'># amcl</span>
|
||||
<span class='fu'>atc_umcg</span>(<span class='st'>"amcl"</span>) <span class='co'># AMCL</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
@ -312,9 +288,11 @@
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
|
||||
<li><a href="#source">Source</a></li>
|
||||
<li><a href="#value">Value</a></li>
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
|
||||
<li><a href="#examples">Examples</a></li>
|
||||
</ul>
|
||||
|
@ -282,7 +282,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
|
||||
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://www.rdocumentation.org/packages/dplyr/topics/n_distinct'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
|
||||
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
|
||||
<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</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>
|
||||
@ -321,13 +321,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</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'>%>%</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'>cipr</span>),
|
||||
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</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'>cipr</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://www.rdocumentation.org/packages/dplyr/topics/n'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount 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>
|
||||
@ -345,13 +345,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='co'># }</span></pre>
|
||||
|
@ -368,11 +368,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='co'># Filter on first isolates:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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='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'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
|
||||
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
|
||||
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</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='co'># Which can be shortened to:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
@ -383,14 +383,14 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<span class='co'># Now let's see if first isolates matter:</span>
|
||||
<span class='no'>A</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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'>gent</span>), <span class='co'># gentamicin availability</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'>%>%</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'>gent</span>), <span class='co'># gentamicin availability</span>
|
||||
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
|
||||
|
||||
<span class='no'>B</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%>%</span> <span class='co'># the 1st isolate filter</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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'>gent</span>), <span class='co'># gentamicin availability</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'>%>%</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'>gent</span>), <span class='co'># gentamicin availability</span>
|
||||
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
|
||||
|
||||
<span class='co'># Have a look at A and B.</span>
|
||||
|
@ -385,34 +385,34 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<span class='co'># you could also use `select` or `pull` to get your variables</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>freq</span>()
|
||||
|
||||
|
||||
<span class='co'># multiple selected variables will be pasted together</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='no'>left_join_microorganisms</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>genus</span>, <span class='no'>species</span>)
|
||||
|
||||
|
||||
<span class='co'># group a variable and analyse another</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>gender</span>)
|
||||
|
||||
|
||||
<span class='co'># get top 10 bugs of hospital A as a vector</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>top_freq</span>(<span class='fl'>10</span>)
|
||||
|
||||
|
||||
<span class='co'># save frequency table to an object</span>
|
||||
<span class='no'>years</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>year</span>)
|
||||
|
||||
|
||||
@ -463,11 +463,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='co'># only get selected columns</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</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'># check differences between frequency tables</span>
|
||||
|
@ -334,7 +334,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</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'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
|
||||
<span class='fu'>geom_rsi</span>()
|
||||
|
||||
<span class='co'># prettify the plot using some additional functions:</span>
|
||||
@ -348,17 +348,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>()
|
||||
|
||||
<span class='co'># get only portions and no counts:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>portion_df</span>)
|
||||
|
||||
<span class='co'># add other ggplot2 parameters as you like:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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>,
|
||||
@ -367,25 +367,25 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<span class='co'># resistance of ciprofloxacine per age group</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</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'>%>%</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'>%>%</span>
|
||||
<span class='co'># `age_group` is also a function of this package:</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>age_group</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'>%>%</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'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
|
||||
<span class='co'># }</span><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>,
|
||||
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
|
||||
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
|
||||
@ -395,22 +395,22 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='co'># genuine analysis: check 2 most prevalent microorganisms</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%>%</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='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%>%</span>
|
||||
<span class='co'># filter on top three bacterial ID's</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%>%</span>
|
||||
<span class='co'># determine first isolates</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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='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'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
|
||||
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
|
||||
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='co'># filter on first isolates</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='co'># get short MO names (like "E. coli")</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>mo</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'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%>%</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='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%>%</span>
|
||||
<span class='co'># select this short name and some antiseptic drugs</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='co'># group by MO</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
|
||||
<span class='co'># plot the thing, putting MOs on the facet</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
|
||||
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</span>,
|
||||
|
@ -341,13 +341,13 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="ab_property.html">ab_property()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_official()</a></code> <code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_trivial_nl()</a></code> <code><a href="ab_property.html">ab_certe()</a></code> <code><a href="ab_property.html">ab_umcg()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> </p>
|
||||
<p><code><a href="atc_property.html">atc_property()</a></code> <code><a href="atc_property.html">atc_official()</a></code> <code><a href="atc_property.html">atc_name()</a></code> <code><a href="atc_property.html">atc_trivial_nl()</a></code> <code><a href="atc_property.html">atc_certe()</a></code> <code><a href="atc_property.html">atc_umcg()</a></code> <code><a href="atc_property.html">atc_tradenames()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of an antibiotic</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="atc_property.html">atc_property()</a></code> <code><a href="atc_property.html">atc_groups()</a></code> <code><a href="atc_property.html">atc_ddd()</a></code> </p>
|
||||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Properties of an ATC code</p></td>
|
||||
</tr><tr>
|
||||
@ -518,6 +518,12 @@
|
||||
<p><code><a href="mo_renamed.html">mo_renamed()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Vector of taxonomic renamed items</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">guess_mo()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Deprecated functions</p></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
@ -334,8 +334,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='co'># set key antibiotics to a new variable</span>
|
||||
<span class='no'>my_patients</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></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'>%>%</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>),
|
||||
<span class='co'># and first WEIGHTED isolates</span>
|
||||
|
@ -295,7 +295,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
|
@ -618,7 +618,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</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'>mdro</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='co'># }</span></pre>
|
||||
</div>
|
||||
|
@ -340,17 +340,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</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'>%>%</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'>portion_S</span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>%>%</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'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/n'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount 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>
|
||||
@ -365,8 +365,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>%>%</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'>portion_S</span>(<span class='no'>cipr</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'>cipr</span>),
|
||||
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</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'>gent</span>),
|
||||
@ -375,22 +375,22 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
|
||||
<span class='co'># }</span><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
|
||||
<span class='no'>my_table</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</span>), <span class='co'># amoxicillin with metronidazole</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'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</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'>amox</span>, <span class='no'>metr</span>))
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
|
@ -341,7 +341,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>x</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>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'>%>%</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'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span>(<span class='st'>"peni"</span>)
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
|
||||
|
||||
@ -350,7 +350,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
<span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>require</a></span>(<span class='no'>ggplot2</span>)) {
|
||||
|
||||
<span class='no'>data</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>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'>%>%</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'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
|
||||
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
|
||||
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
|
Reference in New Issue
Block a user