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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9123</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9125</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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</dl></div><div class="section level2">
<h2 id="preparing-data-microorganisms">Preparing data: microorganisms<a class="anchor" aria-label="anchor" href="#preparing-data-microorganisms"></a></h2>
<div class="section-desc"><p>These functions are meant to get taxonomically valid properties of microorganisms from any input, but also properties derived from taxonomy, such as the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) , or <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganisms, and use `add_custom_microorganisms() to add your own custom microorganisms to this package.</p></div>
<div class="section-desc"><p>These functions are meant to get taxonomically valid properties of microorganisms from any input, but also properties derived from taxonomy, such as the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) , or <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganisms, and use <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add your own custom microorganisms to this package.</p></div>
</div><div class="section level2">
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</dl></div><div class="section level2">
<h2 id="analysing-data">Analysing data<a class="anchor" aria-label="anchor" href="#analysing-data"></a></h2>
<div class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. With <code><a href="../reference/antibiogram.html">antibiogram()</a></code>, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination antibiogram(WISCA). This function also comes with support for R Markdown and Quarto. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></div>
<div class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. With <code><a href="../reference/antibiogram.html">antibiogram()</a></code>, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination antibiogram(WISCA). This function also comes with support for R Markdown and Quarto. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antimicrobial_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></div>
</div><div class="section level2">
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<dd>Determine Bug-Drug Combinations</dd>
</dl><dl><dt>
<code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">ab_selector()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">aminopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">antifungals()</a></code> <code><a href="antibiotic_class_selectors.html">antimycobacterials()</a></code> <code><a href="antibiotic_class_selectors.html">betalactams()</a></code> <code><a href="antibiotic_class_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">lincosamides()</a></code> <code><a href="antibiotic_class_selectors.html">lipoglycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">nitrofurans()</a></code> <code><a href="antibiotic_class_selectors.html">oxazolidinones()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">phenicols()</a></code> <code><a href="antibiotic_class_selectors.html">polymyxins()</a></code> <code><a href="antibiotic_class_selectors.html">quinolones()</a></code> <code><a href="antibiotic_class_selectors.html">rifamycins()</a></code> <code><a href="antibiotic_class_selectors.html">streptogramins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> <code><a href="antibiotic_class_selectors.html">trimethoprims()</a></code> <code><a href="antibiotic_class_selectors.html">ureidopenicillins()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_per_os()</a></code> <code><a href="antibiotic_class_selectors.html">administrable_iv()</a></code> <code><a href="antibiotic_class_selectors.html">not_intrinsic_resistant()</a></code>
<code><a href="antimicrobial_class_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_class_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_class_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_class_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_class_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_class_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_class_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_class_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_class_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_class_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_class_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_class_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_class_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_class_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_class_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_class_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_class_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_class_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_class_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_class_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_class_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_class_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_class_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_class_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_class_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_class_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_class_selectors.html">not_intrinsic_resistant()</a></code>
</dt>
<dd>Antibiotic Selectors</dd>
<dd>Antimicrobial Selectors</dd>
</dl><dl><dt>
<code><a href="mean_amr_distance.html">mean_amr_distance()</a></code> <code><a href="mean_amr_distance.html">amr_distance_from_row()</a></code>