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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="">2.1.1.9021</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9022</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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<div class="section level2">
<h2 id="introduction-to-the-package">Introduction to the package<a class="anchor" aria-label="anchor" href="#introduction-to-the-package"></a></h2>
<p class="section-desc"></p><p>Please find the introduction to (and some general information about) our package here.</p>
<div class="section-desc"><p>Please find the introduction to (and some general information about) our package here.</p></div>
</div><div id="" class="section level2">
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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>
<p class="section-desc"></p><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 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><div id="" class="section level2">
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</dl></div><div class="section level2">
<h2 id="preparing-data-antibiotics">Preparing data: antibiotics<a class="anchor" aria-label="anchor" href="#preparing-data-antibiotics"></a></h2>
<p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
<div class="section-desc"><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p></div>
</div><div id="" class="section level2">
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</dl></div><div class="section level2">
<h2 id="preparing-data">Preparing data<a class="anchor" aria-label="anchor" href="#preparing-data"></a></h2>
<p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
<div class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></div>
</div><div id="" 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>
<p class="section-desc"></p><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 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><div id="" class="section level2">
@ -350,7 +350,7 @@
</dl></div><div class="section level2">
<h2 id="plotting-data">Plotting data<a class="anchor" aria-label="anchor" href="#plotting-data"></a></h2>
<p class="section-desc"></p><p>Use these functions for the plotting part. The <code>scale_*_mic()</code> functions extend the ggplot2 package to allow plotting of MIC values, even within a manually set range. If using <code><a href="../reference/plot.html">plot()</a></code> (base R) or <code>autoplot()</code> (ggplot2) on MIC values or disk diffusion values, the user can set the interpretation guideline to give the bars the right SIR colours. The <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> function is a short wrapper for users not much accustomed to ggplot2 yet. The <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function is a specific function to plot so-called biplots for PCA (principal component analysis).</p>
<div class="section-desc"><p>Use these functions for the plotting part. The <code>scale_*_mic()</code> functions extend the ggplot2 package to allow plotting of MIC values, even within a manually set range. If using <code><a href="../reference/plot.html">plot()</a></code> (base R) or <code>autoplot()</code> (ggplot2) on MIC values or disk diffusion values, the user can set the interpretation guideline to give the bars the right SIR colours. The <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> function is a short wrapper for users not much accustomed to ggplot2 yet. The <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function is a specific function to plot so-called biplots for PCA (principal component analysis).</p></div>
</div><div id="" class="section level2">
@ -376,7 +376,7 @@
</dl></div><div class="section level2">
<h2 id="other-amr-specific-options">Other: AMR-specific options<a class="anchor" aria-label="anchor" href="#other-amr-specific-options"></a></h2>
<p class="section-desc"></p><p>The AMR package is customisable, by providing settings that can be set per user or per team. For example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported language can be set for the whole team (system-language independent) for antibiotic names in a foreign language.</p>
<div class="section-desc"><p>The AMR package is customisable, by providing settings that can be set per user or per team. For example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported language can be set for the whole team (system-language independent) for antibiotic names in a foreign language.</p></div>
</div><div id="" class="section level2">
@ -392,7 +392,7 @@
</dl></div><div class="section level2">
<h2 id="other-antiviral-drugs">Other: antiviral drugs<a class="anchor" aria-label="anchor" href="#other-antiviral-drugs"></a></h2>
<p class="section-desc"></p><p>This package also provides extensive support for antiviral agents, even though it is not the primary scope of this package. Working with data containing information about antiviral drugs was never easier. Use these functions to get valid properties of antiviral drugs from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/av_from_text.html">av_from_text()</a></code>.</p>
<div class="section-desc"><p>This package also provides extensive support for antiviral agents, even though it is not the primary scope of this package. Working with data containing information about antiviral drugs was never easier. Use these functions to get valid properties of antiviral drugs from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/av_from_text.html">av_from_text()</a></code>.</p></div>
</div><div id="" class="section level2">
@ -418,7 +418,7 @@
</dl></div><div class="section level2">
<h2 id="other-background-information-on-included-data">Other: background information on included data<a class="anchor" aria-label="anchor" href="#other-background-information-on-included-data"></a></h2>
<p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p>
<div class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></div>
</div><div id="" class="section level2">
@ -484,7 +484,7 @@
</dl></div><div class="section level2">
<h2 id="other-miscellaneous-functions">Other: miscellaneous functions<a class="anchor" aria-label="anchor" href="#other-miscellaneous-functions"></a></h2>
<p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p>
<div class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></div>
</div><div id="" class="section level2">
@ -545,7 +545,7 @@
</dl></div><div class="section level2">
<h2 id="other-statistical-tests">Other: statistical tests<a class="anchor" aria-label="anchor" href="#other-statistical-tests"></a></h2>
<p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p>
<div class="section-desc"><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p></div>
</div><div id="" class="section level2">
@ -574,11 +574,11 @@
<footer><div class="pkgdown-footer-left">
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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