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(v1.8.1.9014) add Toxoplasma

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dr. M.S. (Matthijs) Berends 2022-08-12 23:27:15 +02:00
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commit ab97268f4c
20 changed files with 808 additions and 728 deletions
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6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.1.9013
Date: 2022-06-10
Version: 1.8.1.9014
Date: 2022-08-12
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
@ -90,5 +90,5 @@ BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.0
RoxygenNote: 7.2.1
Roxygen: list(markdown = TRUE)

4
NEWS.md
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# `AMR` 1.8.1.9013
## <small>Last updated: 10 June 2022</small>
# `AMR` 1.8.1.9014
## <small>Last updated: 12 August 2022</small>
### New
* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.

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docs/404.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -210,7 +210,7 @@ Content not found. Please use links in the navbar.
<div class="pkgdown">
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer>

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docs/LICENSE-text.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -420,7 +420,7 @@ END OF TERMS AND CONDITIONS
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

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docs/articles/datasets.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">10 June 2022</h4>
<h4 data-toc-skip class="date">12 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -224,7 +224,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</e
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 June 2022 11:09:45 UTC. Find more info
<p>It was last updated on 13 June 2022 13:55:27 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1481,7 +1481,7 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<div class="pkgdown">
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer>

4
docs/authors.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -273,7 +273,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

44
docs/index.html
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@ -47,7 +47,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -214,17 +214,17 @@
<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
</h5>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,
<span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
<span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
<span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span>
<span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span>
<span> <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<table class="table">
<thead><tr class="header">
@ -331,10 +331,10 @@
</table>
<p>A base R equivalent would be, giving the exact same results:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span>
<span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,
<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
<code class="sourceCode R"><span><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span></span>
<span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span></span>
<span> <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></code></pre></div>
</div>
<div class="section level4">
<h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
@ -377,7 +377,7 @@
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
@ -390,14 +390,14 @@
<li>
<p>Manually, using:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
</li>
<li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,</span>
<span> msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
</li>
</ol>
@ -562,7 +562,7 @@
<div class="pkgdown">
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer>

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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -162,53 +162,76 @@
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.mo</span><span class="op">(</span>
<span class="va">x</span>,
Becker <span class="op">=</span> <span class="cn">FALSE</span>,
Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,
allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,
reference_df <span class="op">=</span> <span class="fu"><a href="mo_source.html">get_mo_source</a></span><span class="op">(</span><span class="op">)</span>,
ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,
<span class="va">...</span>
<span class="op">)</span>
<span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span>
<span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span>
<span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.mo</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> Becker <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> reference_df <span class="op">=</span> <span class="fu"><a href="mo_source.html">get_mo_source</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">is.mo</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_failures</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with one or two columns</p></dd>
<dt>Becker</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2,3).</p>
<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></dd>
<dt>Lancefield</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a beta-haemolytic <em>Streptococcus</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
<p>This excludes enterococci at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all enterococci as group D.</p></dd>
<dt>allow_uncertain</dt>
<dd><p>a number between <code>0</code> (or <code>"none"</code>) and <code>3</code> (or <code>"all"</code>), or <code>TRUE</code> (= <code>2</code>) or <code>FALSE</code> (= <code>0</code>) to indicate whether the input should be checked for less probable results, see <em>Details</em></p></dd>
<dt>reference_df</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href="mo_source.html">set_mo_source()</a></code> and <code><a href="mo_source.html">get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></dd>
<dt>ignore_pattern</dt>
<dd><p>a regular expression (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the option <code>AMR_ignore_pattern</code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd>
<dt>language</dt>
<dd><p>language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
<dd><p>other arguments passed on to functions</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>mo</code></p>
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></p>
<p></p>
<p><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>mo</code></p>
</div>
<div id="details">
<h2>Details</h2>
@ -218,7 +241,18 @@
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p>
<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> Code Full name</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="sc">---------------</span> <span class="sc">--------------------------------------</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> B_KLBSL Klebsiella</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> B_KLBSL_PNMN Klebsiella pneumoniae</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="er">|</span> <span class="er">|</span> <span class="er">|</span> \<span class="sc">--</span><span class="ot">-&gt;</span> subspecies, a <span class="dv">4-5</span> letter acronym</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> <span class="er">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> species, a <span class="dv">4-5</span> letter acronym</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="sc">|</span> \<span class="sc">---</span><span class="ot">-&gt;</span> genus, a <span class="dv">5-7</span> letter acronym</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> \<span class="sc">---</span><span class="ot">-&gt;</span> taxonomic kingdom<span class="sc">:</span> <span class="fu">A</span> (Archaea), <span class="fu">AN</span> (Animalia), <span class="fu">B</span> (Bacteria),</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">C</span> (Chromista), <span class="fu">F</span> (Fungi), <span class="fu">P</span> (Protozoa)</span></code></pre><p></p></div>
<p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href="mo_property.html">mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href="microorganisms.html">microorganisms</a>).</p>
@ -318,44 +352,43 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span>
<span class="co"># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span> <span class="co"># WHONET code</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Zthafilokkoockus oureuz"</span><span class="op">)</span> <span class="co"># handles incorrect spelling</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span>
<span class="co"># Dyslexia is no problem - these all work:</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticum"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticus"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasmium urealytica"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplazma urealitycium"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"GAS"</span><span class="op">)</span> <span class="co"># Group A Streptococci</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"GBS"</span><span class="op">)</span> <span class="co"># Group B Streptococci</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span>
<span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span>
<span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
<span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span>
<span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span>
<span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"vanco"</span><span class="op">)</span> <span class="co"># returns TRUE</span>
<span class="co"># }</span>
</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># \donttest{</span></span>
<span><span class="co"># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span> <span class="co"># WHONET code</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Zthafilokkoockus oureuz"</span><span class="op">)</span> <span class="co"># handles incorrect spelling</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span></span>
<span></span>
<span><span class="co"># Dyslexia is no problem - these all work:</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticum"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasma urealyticus"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplasmium urealytica"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Ureaplazma urealitycium"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GAS"</span><span class="op">)</span> <span class="co"># Group A Streptococci</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"GBS"</span><span class="op">)</span> <span class="co"># Group B Streptococci</span></span>
<span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span>
<span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span>
<span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span></span>
<span></span>
<span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span>
<span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span></span>
<span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span></span>
<span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"vanco"</span><span class="op">)</span> <span class="co"># returns TRUE</span></span>
<span><span class="co"># }</span></span></code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -369,7 +402,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

4
docs/reference/index.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -416,7 +416,7 @@
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

140
docs/reference/key_antimicrobials.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -162,59 +162,82 @@
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">key_antimicrobials</span><span class="op">(</span>
x <span class="op">=</span> <span class="cn">NULL</span>,
col_mo <span class="op">=</span> <span class="cn">NULL</span>,
universal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"amoxicillin/clavulanic acid"</span>, <span class="st">"cefuroxime"</span>,
<span class="st">"piperacillin/tazobactam"</span>, <span class="st">"ciprofloxacin"</span>, <span class="st">"trimethoprim/sulfamethoxazole"</span><span class="op">)</span>,
gram_negative <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"gentamicin"</span>, <span class="st">"tobramycin"</span>, <span class="st">"colistin"</span>, <span class="st">"cefotaxime"</span>,
<span class="st">"ceftazidime"</span>, <span class="st">"meropenem"</span><span class="op">)</span>,
gram_positive <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"vancomycin"</span>, <span class="st">"teicoplanin"</span>, <span class="st">"tetracycline"</span>, <span class="st">"erythromycin"</span>,
<span class="st">"oxacillin"</span>, <span class="st">"rifampin"</span><span class="op">)</span>,
antifungal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anidulafungin"</span>, <span class="st">"caspofungin"</span>, <span class="st">"fluconazole"</span>, <span class="st">"miconazole"</span>,
<span class="st">"nystatin"</span>, <span class="st">"voriconazole"</span><span class="op">)</span>,
only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,
<span class="va">...</span>
<span class="op">)</span>
<span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">antimicrobials_equal</span><span class="op">(</span>
<span class="va">y</span>,
<span class="va">z</span>,
type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"points"</span>, <span class="st">"keyantimicrobials"</span><span class="op">)</span>,
ignore_I <span class="op">=</span> <span class="cn">TRUE</span>,
points_threshold <span class="op">=</span> <span class="fl">2</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">key_antimicrobials</span><span class="op">(</span></span>
<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> universal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"amoxicillin/clavulanic acid"</span>, <span class="st">"cefuroxime"</span>,</span>
<span> <span class="st">"piperacillin/tazobactam"</span>, <span class="st">"ciprofloxacin"</span>, <span class="st">"trimethoprim/sulfamethoxazole"</span><span class="op">)</span>,</span>
<span> gram_negative <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"gentamicin"</span>, <span class="st">"tobramycin"</span>, <span class="st">"colistin"</span>, <span class="st">"cefotaxime"</span>, <span class="st">"ceftazidime"</span>,</span>
<span> <span class="st">"meropenem"</span><span class="op">)</span>,</span>
<span> gram_positive <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"vancomycin"</span>, <span class="st">"teicoplanin"</span>, <span class="st">"tetracycline"</span>, <span class="st">"erythromycin"</span>,</span>
<span> <span class="st">"oxacillin"</span>, <span class="st">"rifampin"</span><span class="op">)</span>,</span>
<span> antifungal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anidulafungin"</span>, <span class="st">"caspofungin"</span>, <span class="st">"fluconazole"</span>, <span class="st">"miconazole"</span>, <span class="st">"nystatin"</span>,</span>
<span> <span class="st">"voriconazole"</span><span class="op">)</span>,</span>
<span> only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span></span>
<span> <span class="va">y</span>,</span>
<span> <span class="va">z</span>,</span>
<span> type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"points"</span>, <span class="st">"keyantimicrobials"</span><span class="op">)</span>,</span>
<span> ignore_I <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> points_threshold <span class="op">=</span> <span class="fl">2</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be left blank to determine automatically</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>universal</dt>
<dd><p>names of <strong>broad-spectrum</strong> antimicrobial agents, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>gram_negative</dt>
<dd><p>names of antibiotic agents for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>gram_positive</dt>
<dd><p>names of antibiotic agents for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>antifungal</dt>
<dd><p>names of antifungal agents for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>only_rsi_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dt>...</dt>
<dd><p>ignored, only in place to allow future extensions</p></dd>
<dt>y, z</dt>
<dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare</p></dd>
<dt>type</dt>
<dd><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dt>ignore_I</dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
<dt>points_threshold</dt>
<dd><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
</dl></div>
<div id="details">
<h2>Details</h2>
@ -267,38 +290,37 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># `example_isolates` is a data set available in the AMR package.</span>
<span class="co"># See ?example_isolates.</span>
<span class="co"># output of the `key_antimicrobials()` function could be like this:</span>
<span class="va">strainA</span> <span class="op">&lt;-</span> <span class="st">"SSSRR.S.R..S"</span>
<span class="va">strainB</span> <span class="op">&lt;-</span> <span class="st">"SSSIRSSSRSSS"</span>
<span class="co"># those strings can be compared with:</span>
<span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span>
<span class="co"># TRUE, because I is ignored (as well as missing values)</span>
<span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span>
<span class="co"># \donttest{</span>
<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="co"># set key antibiotics to a new variable</span>
<span class="va">my_patients</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>
<span class="co"># now calculate first isolates</span>
first_regular <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,
<span class="co"># and first WEIGHTED isolates</span>
first_weighted <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="st">"keyab"</span><span class="op">)</span>
<span class="op">)</span>
<span class="co"># Check the difference, in this data set it results in more isolates:</span>
<span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
<span class="op">}</span>
<span class="co"># }</span>
</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span>
<span><span class="co"># See ?example_isolates.</span></span>
<span></span>
<span><span class="co"># output of the `key_antimicrobials()` function could be like this:</span></span>
<span><span class="va">strainA</span> <span class="op">&lt;-</span> <span class="st">"SSSRR.S.R..S"</span></span>
<span><span class="va">strainB</span> <span class="op">&lt;-</span> <span class="st">"SSSIRSSSRSSS"</span></span>
<span></span>
<span><span class="co"># those strings can be compared with:</span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span></span>
<span><span class="co"># TRUE, because I is ignored (as well as missing values)</span></span>
<span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span></span>
<span></span>
<span><span class="co"># \donttest{</span></span>
<span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="co"># set key antibiotics to a new variable</span></span>
<span> <span class="va">my_patients</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
<span> <span class="co"># now calculate first isolates</span></span>
<span> first_regular <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="co"># and first WEIGHTED isolates</span></span>
<span> first_weighted <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="st">"keyab"</span><span class="op">)</span></span>
<span> <span class="op">)</span></span>
<span> </span>
<span> <span class="co"># Check the difference, in this data set it results in more isolates:</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="op">}</span></span>
<span><span class="co"># }</span></span></code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -312,7 +334,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

20
docs/reference/mo_matching_score.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -162,15 +162,18 @@
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_matching_score</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_matching_score</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>Any user input value(s)</p></dd>
<dt>n</dt>
<dd><p>A full taxonomic name, that exists in <code><a href="microorganisms.html">microorganisms$fullname</a></code></p></dd>
</dl></div>
<div id="matching-score-for-microorganisms">
<h2>Matching Score for Microorganisms</h2>
@ -216,12 +219,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu">mo_matching_score</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"E. coli"</span>,
n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span><span class="op">)</span>
</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span>
<span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_matching_score</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"E. coli"</span>,</span>
<span> n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -235,7 +237,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

336
docs/reference/mo_property.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -162,83 +162,96 @@
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_type</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_gram_negative</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_yeast</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span><span class="va">x</span>, <span class="va">ab</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_snomed</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_ref</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_authors</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_year</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_lpsn</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_type</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_gram_negative</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_yeast</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span><span class="va">x</span>, <span class="va">ab</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_snomed</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_ref</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_authors</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_year</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code>. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see <em>Examples</em>.</p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Also used to translate text like "no growth". Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>...</dt>
<dd><p>other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'allow_uncertain' and 'ignore_pattern'</p></dd>
<dt>ab</dt>
<dd><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>open</dt>
<dd><p>browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">browseURL()</a></code></p></dd>
<dt>property</dt>
<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "species_id", "source", "prevalence" or "snomed", or must be <code>"shortname"</code></p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
<li><p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
<li><p>A named <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in case of <code>mo_url()</code></p></li>
<li><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> in case of <code>mo_snomed()</code></p></li>
@ -322,108 +335,107 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># taxonomic tree -----------------------------------------------------------</span>
<span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria"</span>
<span class="fu">mo_phylum</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Proteobacteria"</span>
<span class="fu">mo_class</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Gammaproteobacteria"</span>
<span class="fu">mo_order</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Enterobacterales"</span>
<span class="fu">mo_family</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Enterobacteriaceae"</span>
<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Escherichia"</span>
<span class="fu">mo_species</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "coli"</span>
<span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># ""</span>
<span class="co"># colloquial properties ----------------------------------------------------</span>
<span class="fu">mo_name</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Escherichia coli"</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Escherichia coli" - same as mo_name()</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "E. coli"</span>
<span class="co"># other properties ---------------------------------------------------------</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Gram-negative"</span>
<span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># 112283007, 116395006, ... (SNOMED codes)</span>
<span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria" (equal to kingdom, but may be translated)</span>
<span class="fu">mo_rank</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "species"</span>
<span class="fu">mo_url</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># get the direct url to the online database entry</span>
<span class="fu">mo_synonyms</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># get previously accepted taxonomic names</span>
<span class="co"># scientific reference -----------------------------------------------------</span>
<span class="fu">mo_ref</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Castellani et al., 1919"</span>
<span class="fu">mo_authors</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Castellani et al."</span>
<span class="fu">mo_year</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># 1919</span>
<span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># 776057 (LPSN record ID)</span>
<span class="co"># abbreviations known in the field -----------------------------------------</span>
<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># "Staphylococcus"</span>
<span class="fu">mo_species</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># "aureus"</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># "S. aureus"</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># "Gram-positive"</span>
<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span> <span class="co"># "Escherichia"</span>
<span class="fu">mo_species</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span> <span class="co"># "coli"</span>
<span class="co"># known subspecies ---------------------------------------------------------</span>
<span class="fu">mo_name</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "Campylobacter jejuni doylei"</span>
<span class="fu">mo_genus</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "Campylobacter"</span>
<span class="fu">mo_species</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "jejuni"</span>
<span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "doylei"</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span> <span class="co"># "Klebsiella pneumoniae rhinoscleromatis"</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span> <span class="co"># "K. pneumoniae"</span>
<span class="co"># \donttest{</span>
<span class="co"># Becker classification, see ?as.mo ----------------------------------------</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span> <span class="co"># "Staphylococcus epidermidis"</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span> <span class="co"># "S. epidermidis"</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "CoNS"</span>
<span class="co"># Lancefield classification, see ?as.mo ------------------------------------</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span> <span class="co"># "Streptococcus pyogenes"</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "Streptococcus group A"</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span> <span class="co"># "S. pyogenes"</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "GAS" (='Group A Streptococci')</span>
<span class="co"># language support --------------------------------------------------------</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># "Gramnegativ"</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># "Gram-negatief"</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># "Gram negativo"</span>
<span class="co"># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
<span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria" on a German system</span>
<span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bakterien" on a German system</span>
<span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria" on an English system</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,
Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,
language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># "Streptococcus Gruppe A"</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,
Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,
language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># "Streptococcus groep A"</span>
<span class="co"># other --------------------------------------------------------------------</span>
<span class="fu">mo_is_yeast</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Candida"</span>, <span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="co"># TRUE, FALSE</span>
<span class="co"># gram stains and intrinsic resistance can also be used as a filter in dplyr verbs</span>
<span class="co"># \donttest{</span>
<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span>
<span class="op">}</span>
<span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span>
<span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="co"># get a list with the taxonomy, the authors, Gram-stain,</span>
<span class="co"># SNOMED codes, and URL to the online database</span>
<span class="fu">mo_info</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="co"># }</span>
<span class="co"># }</span>
</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># taxonomic tree -----------------------------------------------------------</span></span>
<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria"</span></span>
<span><span class="fu">mo_phylum</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Proteobacteria"</span></span>
<span><span class="fu">mo_class</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Gammaproteobacteria"</span></span>
<span><span class="fu">mo_order</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Enterobacterales"</span></span>
<span><span class="fu">mo_family</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Enterobacteriaceae"</span></span>
<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Escherichia"</span></span>
<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "coli"</span></span>
<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># ""</span></span>
<span></span>
<span><span class="co"># colloquial properties ----------------------------------------------------</span></span>
<span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Escherichia coli"</span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Escherichia coli" - same as mo_name()</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "E. coli"</span></span>
<span></span>
<span><span class="co"># other properties ---------------------------------------------------------</span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Gram-negative"</span></span>
<span><span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># 112283007, 116395006, ... (SNOMED codes)</span></span>
<span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria" (equal to kingdom, but may be translated)</span></span>
<span><span class="fu">mo_rank</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "species"</span></span>
<span><span class="fu">mo_url</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># get the direct url to the online database entry</span></span>
<span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># get previously accepted taxonomic names</span></span>
<span></span>
<span><span class="co"># scientific reference -----------------------------------------------------</span></span>
<span><span class="fu">mo_ref</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Castellani et al., 1919"</span></span>
<span><span class="fu">mo_authors</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Castellani et al."</span></span>
<span><span class="fu">mo_year</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># 1919</span></span>
<span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># 776057 (LPSN record ID)</span></span>
<span></span>
<span><span class="co"># abbreviations known in the field -----------------------------------------</span></span>
<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># "Staphylococcus"</span></span>
<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># "aureus"</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># "S. aureus"</span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># "Gram-positive"</span></span>
<span></span>
<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span> <span class="co"># "Escherichia"</span></span>
<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span> <span class="co"># "coli"</span></span>
<span></span>
<span><span class="co"># known subspecies ---------------------------------------------------------</span></span>
<span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "Campylobacter jejuni doylei"</span></span>
<span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "Campylobacter"</span></span>
<span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "jejuni"</span></span>
<span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"doylei"</span><span class="op">)</span> <span class="co"># "doylei"</span></span>
<span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span> <span class="co"># "Klebsiella pneumoniae rhinoscleromatis"</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span> <span class="co"># "K. pneumoniae"</span></span>
<span></span>
<span><span class="co"># \donttest{</span></span>
<span><span class="co"># Becker classification, see ?as.mo ----------------------------------------</span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span> <span class="co"># "Staphylococcus epidermidis"</span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "Coagulase-negative Staphylococcus (CoNS)"</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span><span class="op">)</span> <span class="co"># "S. epidermidis"</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "CoNS"</span></span>
<span></span>
<span><span class="co"># Lancefield classification, see ?as.mo ------------------------------------</span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span> <span class="co"># "Streptococcus pyogenes"</span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "Streptococcus group A"</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span><span class="op">)</span> <span class="co"># "S. pyogenes"</span></span>
<span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"S. pyo"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "GAS" (='Group A Streptococci')</span></span>
<span></span>
<span></span>
<span><span class="co"># language support --------------------------------------------------------</span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># "Gramnegativ"</span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># "Gram-negatief"</span></span>
<span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># "Gram negativo"</span></span>
<span></span>
<span><span class="co"># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span></span>
<span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria" on a German system</span></span>
<span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bakterien" on a German system</span></span>
<span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># "Bacteria" on an English system</span></span>
<span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span>
<span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># "Streptococcus Gruppe A"</span></span>
<span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span>
<span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># "Streptococcus groep A"</span></span>
<span></span>
<span></span>
<span><span class="co"># other --------------------------------------------------------------------</span></span>
<span></span>
<span><span class="fu">mo_is_yeast</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Candida"</span>, <span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="co"># TRUE, FALSE</span></span>
<span></span>
<span><span class="co"># gram stains and intrinsic resistance can also be used as a filter in dplyr verbs</span></span>
<span><span class="co"># \donttest{</span></span>
<span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span> </span>
<span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="op">}</span></span>
<span></span>
<span></span>
<span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span>
<span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span>
<span><span class="co"># get a list with the taxonomy, the authors, Gram-stain,</span></span>
<span><span class="co"># SNOMED codes, and URL to the online database</span></span>
<span><span class="fu">mo_info</span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span>
<span><span class="co"># }</span></span>
<span><span class="co"># }</span></span></code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -437,7 +449,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

23
docs/reference/rsi_translation.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -162,7 +162,7 @@
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">rsi_translation</span></span></code></pre></div>
</div>
<div id="format">
@ -182,8 +182,21 @@
<div id="details">
<h2>Details</h2>
<p>Overview of the data set:</p>
<p></p><div class="sourceCode r"><pre><code><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></code></pre><p></p></div>
<p></p><div class="sourceCode"><pre><code></code></pre><p></p></div>
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></span>
<span><span class="co">#&gt; guideline method site mo rank_index ab ref_tbl disk_dose</span></span>
<span><span class="co">#&gt; 1 EUCAST 2022 MIC &lt;NA&gt; F_ASPRG_MGTS 2 AMB Aspergillus &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 2 EUCAST 2022 MIC &lt;NA&gt; F_ASPRG_NIGR 2 AMB Aspergillus &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 3 EUCAST 2022 MIC &lt;NA&gt; F_CANDD 3 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 4 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_ALBC 2 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 5 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_DBLN 2 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; 6 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_KRUS 2 AMB Candida &lt;NA&gt;</span></span>
<span><span class="co">#&gt; breakpoint_S breakpoint_R uti</span></span>
<span><span class="co">#&gt; 1 1 1 FALSE</span></span>
<span><span class="co">#&gt; 2 1 1 FALSE</span></span>
<span><span class="co">#&gt; 3 1 1 FALSE</span></span>
<span><span class="co">#&gt; 4 1 1 FALSE</span></span>
<span><span class="co">#&gt; 5 1 1 FALSE</span></span>
<span><span class="co">#&gt; 6 1 1 FALSE</span></span></code></pre><p></p></div>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the <code>mo</code> and <code>ab</code> columns have been transformed to contain the full official names instead of codes.</p>
</div>
<div id="reference-data-publicly-available">
@ -215,7 +228,7 @@
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

4
docs/survey.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9014</span>
</span>
</div>
@ -172,7 +172,7 @@
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>
</footer></div>

8
man/key_antimicrobials.Rd
View File

@ -11,12 +11,12 @@ key_antimicrobials(
col_mo = NULL,
universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
"piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime",
"ceftazidime", "meropenem"),
gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime", "ceftazidime",
"meropenem"),
gram_positive = c("vancomycin", "teicoplanin", "tetracycline", "erythromycin",
"oxacillin", "rifampin"),
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
"nystatin", "voriconazole"),
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole", "nystatin",
"voriconazole"),
only_rsi_columns = FALSE,
...
)

30
man/rsi_translation.Rd
View File

@ -30,22 +30,20 @@ Data set containing reference data to interpret MIC and disk diffusion to R/SI v
Overview of the data set:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
}\if{html}{\out{</div>}}
\if{html}{\out{<div class="sourceCode">}}\preformatted{## guideline method site mo rank_index ab ref_tbl disk_dose
## 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
## 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
## 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
## 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
## 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
## 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
## breakpoint_S breakpoint_R uti
## 1 1 1 FALSE
## 2 1 1 FALSE
## 3 1 1 FALSE
## 4 1 1 FALSE
## 5 1 1 FALSE
## 6 1 1 FALSE
#> guideline method site mo rank_index ab ref_tbl disk_dose
#> 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
#> 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
#> 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
#> 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
#> 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
#> 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
#> breakpoint_S breakpoint_R uti
#> 1 1 1 FALSE
#> 2 1 1 FALSE
#> 3 1 1 FALSE
#> 4 1 1 FALSE
#> 5 1 1 FALSE
#> 6 1 1 FALSE
}\if{html}{\out{</div>}}
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.