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<pre> GNU GENERAL PUBLIC LICENSE
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Copyright (C) 1989, 1991 Free Software Foundation, Inc., &lt;http://fsf.org/&gt;
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GNU GENERAL PUBLIC LICENSE
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NO WARRANTY
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END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
{description}
Copyright (C) {year} {fullname}
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
{signature of Ty Coon}, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.
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<h1>The AMR package - How to conduct AMR analysis</h1>
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<p><strong><a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a></strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
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<p><strong>Erwin E. A. Hassing</strong>. Contributor.
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<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
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<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
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<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
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<div id="amr-for-r" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#amr-for-r" class="anchor"></a><code>AMR</code> (for R) <img src="reference/figures/logo.png" align="right" height="120px">
</h1></div>
<p><em>(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
<hr>
<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of <strong>Antimicrobial Resistance (AMR)</strong> and to work with antibiotic properties by using evidence-based methods.</p>
<p>We created this package for academic research at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). We released this under the GNU General Public Licence v2.0 (GPL-2) which makes it free for everybody to use and distribute, for personal and commercial use, but it may <strong>not</strong> be used for patent purposes. Read further about our GPL-2 licence <a href="./LICENSE-text.html">here</a>.</p>
<p>This package is ready-to-use for a professional environment by specialists in the following fields:</p>
<ul>
<li>Medical Microbiology
<ul>
<li>Epidemiologists (both clinical microbiological and research)</li>
<li>Research Microbiologists</li>
<li>Biomedical Researchers</li>
<li>Research Pharmacologists</li>
</ul>
</li>
<li>Veterinary Microbiology
<ul>
<li>Research Veterinarians</li>
<li>Veterinary Epidemiologists</li>
<li>Biomedical Researchers</li>
</ul>
</li>
<li>Microbial Ecology
<ul>
<li>Soil Microbiologists</li>
<li>Extremophile Researchers</li>
<li>Astrobiologists</li>
</ul>
</li>
<li>Other specialists in any of the above fields:
<ul>
<li>Data Scientists/Data Analysts</li>
<li>Biotechnologists</li>
<li>Biochemists</li>
<li>Geneticists</li>
<li>Molecular Biologists/Microbiologists</li>
</ul>
</li>
<li>Developers
<ul>
<li>Package developers for R</li>
<li>Software developers</li>
<li>Web application developers</li>
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</li>
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<div id="get-this-package" class="section level3">
<h3 class="hasAnchor">
<a href="#get-this-package" class="anchor"></a>Get this package</h3>
<p>This package is available on the official R network. Install this package in R with:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
<p>It will be downloaded and installed automatically.</p>
</div>
<div id="get-started" class="section level3">
<h3 class="hasAnchor">
<a href="#get-started" class="anchor"></a>Get started</h3>
<p>To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the button ‘Get Started’ in the top menu.</p>
<hr>
<p><a href="https://www.rug.nl"><img src="./logo_rug.png" height="60px"></a> <a href="https://www.umcg.nl"><img src="./logo_umcg.png" height="60px"></a> <a href="https://www.certe.nl"><img src="./logo_certe.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" height="60px"></a></p>
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<h2>Links</h2>
<ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://​cloud.r-project.org/​package=AMR</a>
</li>
<li>Report a bug at <br><a href="https://gitlab.com/msberends/AMR/issues">https://​gitlab.com/​msberends/​AMR/​issues</a>
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<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, reviewer </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li><a href="authors.html">All authors...</a></li>
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
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<h1>Changelog <small></small></h1>
</div>
<div id="amr-0-5-0-90xx" class="section level1">
<h1 class="page-header">
<a href="#amr-0-5-0-90xx" class="anchor"></a>AMR 0.5.0.90xx<small> Unreleased </small>
</h1>
<p><strong>Note: this is the development version, which will eventually be released as AMR 0.6.0.</strong></p>
<div id="new" class="section level4">
<h4 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code>as.mo</code> to identify an MO code.</li>
<li>New website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
</ul>
</li>
<li>Support for <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>Function <code>mo_failures</code> to review values that could not be coerced to a valid MO code, using <code>as.mo</code>. This latter function will now only show a maximum of 25 uncoerced values.</li>
<li>Function <code>mo_renamed</code> to get a list of all returned values from <code>as.mo</code> that have had taxonomic renaming</li>
<li>Function <code>age</code> to calculate the (patients) age in years</li>
<li>Function <code>age_groups</code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>
<p>Functions <code>filter_first_isolate</code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>()</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients)</a></code></pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
</li>
</ul>
</div>
<div id="changed" class="section level4">
<h4 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h4>
<ul>
<li>Improvements for <code>as.mo</code>:
<ul>
<li>Finds better results when input is in other languages</li>
<li>Better handling for subspecies</li>
<li>Better handling for <em>Salmonellae</em>
</li>
<li>There will be looked for uncertain results at default - these results will be returned with an informative warning</li>
<li>Manual now contains more info about the algorithms</li>
<li>Progress bar will be shown when it takes more than 3 seconds to get results</li>
<li>Support for formatted console text</li>
</ul>
</li>
<li>Function <code>first_isolate</code>:
<ul>
<li>Will now use a column named like “patid” for the patient ID (parameter <code>col_patientid</code>), when this parameter was left blank</li>
<li>Will now use a column named like “key(…)ab” or “key(…)antibiotics” for the key antibiotics (parameter <code>col_keyantibiotics</code>), when this parameter was left blank</li>
<li>Removed parameter <code>output_logical</code>, the function will now always return a logical value</li>
<li>Renamed parameter <code>filter_specimen</code> to <code>specimen_group</code>, although using <code>filter_specimen</code> will still work</li>
</ul>
</li>
<li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li>
<li>Function <code>mo_taxonomy</code> now contains the kingdom too</li>
<li>Function <code>first_isolate</code> will now use a column named like “patid” for the patient ID, when this parameter was left blank</li>
<li>Reduce false positives for <code>is.rsi.eligible</code>
</li>
<li>Summaries of class <code>mo</code> will now return the top 3 and the unique count, e.g. using <code><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary(mo)</a></code>
</li>
<li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code>
</li>
<li>Frequency tables (<code>freq</code> function):
<ul>
<li>Header info is now available as a list, with the <code>header</code> function</li>
<li>Added header info for class <code>mo</code> to show unique count of families, genera and species</li>
<li>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code><a href="https://www.rdocumentation.org/packages/base/topics/options">getOption("OutDec")</a></code>
</li>
<li>The new <code>big.mark</code> parameter will at default be <code>","</code> when <code>decimal.mark = "."</code> and <code>"."</code> otherwise</li>
<li>Fix for header text where all observations are <code>NA</code>
</li>
<li>New parameter <code>droplevels</code> to exclude empty factor levels when input is a factor</li>
<li>Factor levels will be in header when present in input data</li>
</ul>
</li>
<li>Function <code>scale_y_percent</code> now contains the <code>limits</code> parameter</li>
<li>Automatic parameter filling for <code>mdro</code>, <code>key_antibiotics</code> and <code>eucast_rules</code>
</li>
<li>Updated examples for resistance prediction (<code>resistance_predict</code> function)</li>
</ul>
</div>
<div id="other" class="section level4">
<h4 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h4>
<ul>
<li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
</ul>
</div>
</div>
<div id="amr-0-5-0" class="section level1">
<h1 class="page-header">
<a href="#amr-0-5-0" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
</h1>
<div id="new-1" class="section level4">
<h4 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h4>
<ul>
<li>Repository moved to GitLab: <a href="https://gitlab.com/msberends/AMR" class="uri">https://gitlab.com/msberends/AMR</a>
</li>
<li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
</li>
<li>Function <code>get_locale</code> to determine language for language-dependent output for some <code>mo_*</code> functions. This is now the default value for their <code>language</code> parameter, by which the system language will be used at default.</li>
<li>Data sets <code>microorganismsDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganisms.oldDT</code> to improve the speed of <code>as.mo</code>. They are for reference only, since they are primarily for internal use of <code>as.mo</code>.</li>
<li>Function <code>read.4D</code> to read from the 4D database of the MMB department of the UMCG</li>
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
</ul>
</div>
<div id="changed-1" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h4>
<ul>
<li>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code>
</li>
<li>
<code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</li>
<li>Big changes to the <code>eucast_rules</code> function:
<ul>
<li>Now also applies rules from the EUCAST ‘Breakpoint tables for bacteria’, version 8.1, 2018, <a href="http://www.eucast.org/clinical_breakpoints/" class="uri">http://www.eucast.org/clinical_breakpoints/</a> (see Source of the function)</li>
<li>New parameter <code>rules</code> to specify which rules should be applied (expert rules, breakpoints, others or all)</li>
<li>New parameter <code>verbose</code> which can be set to <code>TRUE</code> to get very specific messages about which columns and rows were affected</li>
<li>Better error handling when rules cannot be applied (i.e. new values could not be inserted)</li>
<li>The number of affected values will now only be measured once per row/column combination</li>
<li>Data set <code>septic_patients</code> now reflects these changes</li>
<li>Added parameter <code>pipe</code> for piperacillin (J01CA12), also to the <code>mdro</code> function</li>
<li>Small fixes to EUCAST clinical breakpoint rules</li>
</ul>
</li>
<li>Added column <code>kingdom</code> to the microorganisms data set, and function <code>mo_kingdom</code> to look up values</li>
<li>Tremendous speed improvement for <code>as.mo</code> (and subsequently all <code>mo_*</code> functions), as empty values wil be ignored <em>a priori</em>
</li>
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
</li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
<li>Added parameter <code>also_single_tested</code> for <code>portion_*</code> and <code>count_*</code> functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see <code><a href="../reference/portion.html">?portion</a></code>
</li>
<li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code>
</li>
<li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li>
<li>Frequency tables - <code><a href="../reference/freq.html">freq()</a></code>:
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li>
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
</li>
<li>Now prints in markdown at default in non-interactive sessions</li>
<li>No longer adds the factor level column and sorts factors on count again</li>
<li>Support for class <code>difftime</code>
</li>
<li>New parameter <code>na</code>, to choose which character to print for empty values</li>
<li>New parameter <code>header</code> to turn the header info off (default when <code>markdown = TRUE</code>)</li>
<li>New parameter <code>title</code> to manually setbthe title of the frequency table</li>
</ul>
</li>
<li>
<code>first_isolate</code> now tries to find columns to use as input when parameters are left blank</li>
<li>Improvements for MDRO algorithm (function <code>mdro</code>)</li>
<li>Data set <code>septic_patients</code> is now a <code>data.frame</code>, not a tibble anymore</li>
<li>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</li>
<li>Fix for <code>mo_property</code> not working properly</li>
<li>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</li>
<li>Support for named vectors of class <code>mo</code>, useful for <code><a href="../reference/freq.html">top_freq()</a></code>
</li>
<li>
<code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</li>
<li>AI improvements for <code>as.mo</code>:
<ul>
<li>
<code>"CRS"</code> -&gt; <em>Stenotrophomonas maltophilia</em>
</li>
<li>
<code>"CRSM"</code> -&gt; <em>Stenotrophomonas maltophilia</em>
</li>
<li>
<code>"MSSA"</code> -&gt; <em>Staphylococcus aureus</em>
</li>
<li>
<code>"MSSE"</code> -&gt; <em>Staphylococcus epidermidis</em>
</li>
</ul>
</li>
<li>Fix for <code>join</code> functions</li>
<li>Speed improvement for <code>is.rsi.eligible</code>, now 15-20 times faster</li>
<li>In <code>g.test</code>, when <code><a href="https://www.rdocumentation.org/packages/base/topics/sum">sum(x)</a></code> is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested</li>
<li>
<code>ab_name</code> will try to fall back on <code>as.atc</code> when no results are found</li>
<li>Removed the addin to view data sets</li>
<li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
</ul>
</div>
<div id="other-1" class="section level4">
<h4 class="hasAnchor">
<a href="#other-1" class="anchor"></a>Other</h4>
<ul>
<li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
<li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
<li>Updated vignettes to comply with README</li>
</ul>
</div>
</div>
<div id="amr-0-4-0" class="section level1">
<h1 class="page-header">
<a href="#amr-0-4-0" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
</h1>
<div id="new-2" class="section level4">
<h4 class="hasAnchor">
<a href="#new-2" class="anchor"></a>New</h4>
<ul>
<li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
<li>New functions based on the existing function <code>mo_property</code>:
<ul>
<li>Taxonomic names: <code>mo_phylum</code>, <code>mo_class</code>, <code>mo_order</code>, <code>mo_family</code>, <code>mo_genus</code>, <code>mo_species</code>, <code>mo_subspecies</code>
</li>
<li>Semantic names: <code>mo_fullname</code>, <code>mo_shortname</code>
</li>
<li>Microbial properties: <code>mo_type</code>, <code>mo_gramstain</code>
</li>
<li>Author and year: <code>mo_ref</code>
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</li>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul>
<li>Extra function <code>count_df</code> (which works like <code>portion_df</code>) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables</li>
</ul>
</li>
<li>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code>
</li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI):</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb8-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb9-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
<ul>
<li>Column names inputs of <code>EUCAST_rules</code>, <code>first_isolate</code> and <code>key_antibiotics</code>
</li>
<li>Column names of datasets <code>microorganisms</code> and <code>septic_patients</code>
</li>
<li>All old syntaxes will still work with this version, but will throw warnings</li>
</ul>
</li>
<li>Function <code>labels_rsi_count</code> to print datalabels on a RSI <code>ggplot2</code> model</li>
<li><p>Functions <code>as.atc</code> and <code>is.atc</code> to transform/look up antibiotic ATC codes as defined by the WHO. The existing function <code>guess_atc</code> is now an alias of <code>as.atc</code>.</p></li>
<li>Function <code>ab_property</code> and its aliases: <code>ab_name</code>, <code>ab_tradenames</code>, <code>ab_certe</code>, <code>ab_umcg</code> and <code>ab_trivial_nl</code>
</li>
<li>Introduction to AMR as a vignette</li>
<li>Removed clipboard functions as it violated the CRAN policy</li>
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
</ul>
</div>
<div id="changed-2" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-2" class="anchor"></a>Changed</h4>
<ul>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="../reference/ab_property.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb10-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb10-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
<li>Fix for <code>as.mic</code> for values ending in zeroes after a real number</li>
<li>Small fix where <em>B. fragilis</em> would not be found in the <code>microorganisms.umcg</code> data set</li>
<li>Added <code>prevalence</code> column to the <code>microorganisms</code> data set</li>
<li>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code>
</li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb11-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb11-4" data-line-number="4"></a>
<a class="sourceLine" id="cb11-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb11-6" data-line-number="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb11-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
</li>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
<li>Added datalabels function <code>labels_rsi_count</code> to <code>ggplot_rsi</code>
</li>
<li>Added possibility to set any parameter to <code>geom_rsi</code> (and <code>ggplot_rsi</code>) so you can set your own preferences</li>
<li>Fix for joins, where predefined suffices would not be honoured</li>
<li>Added parameter <code>quote</code> to the <code>freq</code> function</li>
<li>Added generic function <code>diff</code> for frequency tables</li>
<li>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code>
</li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb13-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb13-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
</ul>
</div>
<div id="other-2" class="section level4">
<h4 class="hasAnchor">
<a href="#other-2" class="anchor"></a>Other</h4>
<ul>
<li>More unit tests to ensure better integrity of functions</li>
</ul>
</div>
</div>
<div id="amr-0-3-0" class="section level1">
<h1 class="page-header">
<a href="#amr-0-3-0" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
</h1>
<div id="new-3" class="section level4">
<h4 class="hasAnchor">
<a href="#new-3" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
<ul>
<li>New function <code>portion_df</code> to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables</li>
</ul>
</li>
<li>
<strong>BREAKING</strong>: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call <em>key antibiotics</em>) to include more first isolates (afterwards called first <em>weighted</em> isolates) are now as follows:
<ul>
<li>Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole</li>
<li>Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin</li>
<li>Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem</li>
</ul>
</li>
<li>Support for <code>ggplot2</code>
<ul>
<li>New functions <code>geom_rsi</code>, <code>facet_rsi</code>, <code>scale_y_percent</code>, <code>scale_rsi_colours</code> and <code>theme_rsi</code>
</li>
<li>New wrapper function <code>ggplot_rsi</code> to apply all above functions on a data set:
<ul>
<li>
<code>septic_patients %&gt;% select(tobr, gent) %&gt;% ggplot_rsi</code> will show portions of S, I and R immediately in a pretty plot</li>
<li>Support for grouped variables, see <code><a href="../reference/ggplot_rsi.html">?ggplot_rsi</a></code>
</li>
</ul>
</li>
</ul>
</li>
<li>Determining bacterial ID:
<ul>
<li>New functions <code>as.bactid</code> and <code>is.bactid</code> to transform/ look up microbial ID’s.</li>
<li>The existing function <code>guess_bactid</code> is now an alias of <code>as.bactid</code>
</li>
<li>New Becker classification for <em>Staphylococcus</em> to categorise them into Coagulase Negative <em>Staphylococci</em> (CoNS) and Coagulase Positve <em>Staphylococci</em> (CoPS)</li>
<li>New Lancefield classification for <em>Streptococcus</em> to categorise them into Lancefield groups</li>
</ul>
</li>
<li>For convience, new descriptive statistical functions <code>kurtosis</code> and <code>skewness</code> that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices</li>
<li>Function <code>g.test</code> to perform the Χ<sup>2</sup> distributed <a href="https://en.wikipedia.org/wiki/G-test"><em>G</em>-test</a>, which use is the same as <code>chisq.test</code>
</li>
<li>
<del>Function <code>ratio</code> to transform a vector of values to a preset ratio</del>
<ul>
<li><del>For example: <code><a href="../reference/AMR-deprecated.html">ratio(c(10, 500, 10), ratio = "1:2:1")</a></code> would return <code>130, 260, 130</code></del></li>
</ul>
</li>
<li>Support for Addins menu in RStudio to quickly insert <code>%in%</code> or <code>%like%</code> (and give them keyboard shortcuts), or to view the datasets that come with this package</li>
<li>Function <code>p.symbol</code> to transform p values to their related symbols: <code>0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code>
</li>
<li>Functions <code>clipboard_import</code> and <code>clipboard_export</code> as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the <code>clipr</code> package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)</li>
<li>New for frequency tables (function <code>freq</code>):
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code><a href="../reference/freq.html">freq(table(x, y))</a></code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://www.rdocumentation.org/packages/graphics/topics/hist">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code><a href="../reference/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
<li>Possibility to globally set the default for the amount of items to print, with <code><a href="https://www.rdocumentation.org/packages/base/topics/options">options(max.print.freq = n)</a></code> where <em>n</em> is your preset value</li>
</ul>
</li>
</ul>
</div>
<div id="changed-3" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-3" class="anchor"></a>Changed</h4>
<ul>
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
<li>More antibiotics added as parameters for EUCAST rules</li>
<li>Updated version of the <code>septic_patients</code> data set to better reflect the reality</li>
<li>Pretty printing for tibbles removed as it is not really the scope of this package</li>
<li>Printing of <code>mic</code> and <code>rsi</code> classes now returns all values - use <code>freq</code> to check distributions</li>
<li>Improved speed of key antibiotics comparison for determining first isolates</li>
<li>Column names for the <code>key_antibiotics</code> function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs</li>
<li>Speed improvement for the <code>abname</code> function</li>
<li>
<code>%like%</code> now supports multiple patterns</li>
<li>Frequency tables are now actual <code>data.frame</code>s with altered console printing to make it look like a frequency table. Because of this, the parameter <code>toConsole</code> is not longer needed.</li>
<li>Fix for <code>freq</code> where the class of an item would be lost</li>
<li>Small translational improvements to the <code>septic_patients</code> dataset and the column <code>bactid</code> now has the new class <code>"bactid"</code>
</li>
<li>Small improvements to the <code>microorganisms</code> dataset (especially for <em>Salmonella</em>) and the column <code>bactid</code> now has the new class <code>"bactid"</code>
</li>
<li>Combined MIC/RSI values will now be coerced by the <code>rsi</code> and <code>mic</code> functions:
<ul>
<li>
<code><a href="../reference/as.rsi.html">as.rsi("&lt;=0.002; S")</a></code> will return <code>S</code>
</li>
<li>
<code><a href="../reference/as.mic.html">as.mic("&lt;=0.002; S")</a></code> will return <code>&lt;=0.002</code>
</li>
</ul>
</li>
<li>Now possible to coerce MIC values with a space between operator and value, i.e. <code><a href="../reference/as.mic.html">as.mic("&lt;= 0.002")</a></code> now works</li>
<li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li>
<li>Added <code>"groups"</code> option for <code><a href="../reference/atc_property.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <a href="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
<li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li>
<li>Improved <code>first_isolate</code> algorithm to exclude isolates where bacteria ID or genus is unavailable</li>
<li>Fix for warning <em>hybrid evaluation forced for row_number</em> (<a href="https://github.com/tidyverse/dplyr/commit/924b62"><code>924b62</code></a>) from the <code>dplyr</code> package v0.7.5 and above</li>
<li>Support for empty values and for 1 or 2 columns as input for <code>guess_bactid</code> (now called <code>as.bactid</code>)
<ul>
<li>So <code>yourdata %&gt;% select(genus, species) %&gt;% as.bactid()</code> now also works</li>
</ul>
</li>
<li>Other small fixes</li>
</ul>
</div>
<div id="other-3" class="section level4">
<h4 class="hasAnchor">
<a href="#other-3" class="anchor"></a>Other</h4>
<ul>
<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
<ul>
<li>Linux and macOS: <a href="https://travis-ci.org/msberends/AMR" class="uri">https://travis-ci.org/msberends/AMR</a>
</li>
<li>Windows: <a href="https://ci.appveyor.com/project/msberends/amr" class="uri">https://ci.appveyor.com/project/msberends/amr</a>
</li>
</ul>
</li>
<li>Added thesis advisors to DESCRIPTION file</li>
</ul>
</div>
</div>
<div id="amr-0-2-0" class="section level1">
<h1 class="page-header">
<a href="#amr-0-2-0" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
</h1>
<div id="new-4" class="section level4">
<h4 class="hasAnchor">
<a href="#new-4" class="anchor"></a>New</h4>
<ul>
<li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="http://dplyr.tidyverse.org/reference/summarise.html">dplyr::summarise</a></code>, see ?rsi</li>
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
<li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant Organisms (MDRO)</strong> with support for country-specific guidelines.
<ul>
<li>Suggest your own via <a href="https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&amp;body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E">https://github.com/msberends/AMR/issues/new</a>
</li>
<li>
<a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance">Exceptional resistances defined by EUCAST</a> are also supported instead of countries alone</li>
<li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for Dutch and German guidelines, respectively</li>
</ul>
</li>
<li>New algorithm to determine weighted isolates, can now be <code>"points"</code> or <code>"keyantibiotics"</code>, see <code><a href="../reference/first_isolate.html">?first_isolate</a></code>
</li>
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
</ul>
</div>
<div id="changed-4" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-4" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
</li>
<li>Renamed dataset <code>bactlist</code> to <code>microorganisms</code>
</li>
<li>Added common abbreviations and trade names to the <code>antibiotics</code> dataset</li>
<li>Added more microorganisms to the <code>microorganisms</code> dataset</li>
<li>Added analysis examples on help page of dataset <code>septic_patients</code>
</li>
<li>Added support for character vector in <code>join</code> functions</li>
<li>Added warnings when a join results in more rows after than before the join</li>
<li>Altered <code>%like%</code> to make it case insensitive</li>
<li>For parameters of functions <code>first_isolate</code> and <code>EUCAST_rules</code> column names are now case-insensitive</li>
<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
</ul>
</div>
<div id="other-4" class="section level4">
<h4 class="hasAnchor">
<a href="#other-4" class="anchor"></a>Other</h4>
<ul>
<li>Expanded <code>README.md</code> with more examples</li>
<li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>
<li>Added unit testing with the <code>testthat</code> package</li>
<li>Added build tests for Linux and macOS using Travis CI (<a href="https://travis-ci.org/msberends/AMR" class="uri">https://travis-ci.org/msberends/AMR</a>)</li>
<li>Added line coverage checking using CodeCov (<a href="https://codecov.io/gh/msberends/AMR/tree/master/R" class="uri">https://codecov.io/gh/msberends/AMR/tree/master/R</a>)</li>
</ul>
</div>
</div>
<div id="amr-0-1-1" class="section level1">
<h1 class="page-header">
<a href="#amr-0-1-1" class="anchor"></a>AMR 0.1.1<small> 2018-03-14 </small>
</h1>
<ul>
<li>
<code>EUCAST_rules</code> applies for amoxicillin even if ampicillin is missing</li>
<li>Edited column names to comply with GLIMS, the laboratory information system</li>
<li>Added more valid MIC values</li>
<li>Renamed ‘Daily Defined Dose’ to ‘Defined Daily Dose’</li>
<li>Added barplots for <code>rsi</code> and <code>mic</code> classes</li>
</ul>
</div>
<div id="amr-0-1-0" class="section level1">
<h1 class="page-header">
<a href="#amr-0-1-0" class="anchor"></a>AMR 0.1.0<small> 2018-02-22 </small>
</h1>
<ul>
<li>First submission to CRAN.</li>
</ul>
</div>
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<p>These functions are <a href='https://www.rdocumentation.org/packages/base/topics/Deprecated'>Deprecated</a>. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.</p>
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<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)</pre>
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<p>This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and ti work with antibiotic properties by using evidence-based methods.</p>
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<p>[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - <a href='rug.nl'>rug.nl</a> <a href='umcg.nl'>umcg.nl</a> <br />
[2] Certe Medical Diagnostics &amp; Advice, Groningen, the Netherlands - <a href='certe.nl'>certe.nl</a></p>
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<h1>Property of an antibiotic</h1>
<div class="hidden name"><code>ab_property.Rd</code></div>
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<p>Use these functions to return a specific property of an antibiotic from the <code><a href='antibiotics.html'>antibiotics</a></code> data set, based on their ATC code. Get such a code with <code><a href='as.atc.html'>as.atc</a></code>.</p>
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<pre class="usage"><span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"official"</span>)
<span class='fu'>ab_atc</span>(<span class='no'>x</span>)
<span class='fu'>ab_official</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>ab_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>ab_trivial_nl</span>(<span class='no'>x</span>)
<span class='fu'>ab_certe</span>(<span class='no'>x</span>)
<span class='fu'>ab_umcg</span>(<span class='no'>x</span>)
<span class='fu'>ab_tradenames</span>(<span class='no'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a (vector of a) valid <code><a href='as.atc.html'>atc</a></code> code or any text that can be coerced to a valid atc with <code><a href='as.atc.html'>as.atc</a></code></p></td>
</tr>
<tr>
<th>property</th>
<td><p>one of the column names of one of the <code><a href='antibiotics.html'>antibiotics</a></code> data set, like <code>"atc"</code> and <code>"official"</code></p></td>
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to English (<code>"en"</code>) and can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Either one of <code>"en"</code> (English) or <code>"nl"</code> (Dutch).</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A vector of values. In case of <code>ab_tradenames</code>, if <code>x</code> is of length one, a vector will be returned. Otherwise a <code><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></code>, with <code>x</code> as names.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='antibiotics.html'>antibiotics</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'>ab_atc</span>(<span class='st'>"amcl"</span>) <span class='co'># J01CR02</span>
<span class='fu'>ab_name</span>(<span class='st'>"amcl"</span>) <span class='co'># Amoxicillin and beta-lactamase inhibitor</span>
<span class='fu'>ab_name</span>(<span class='st'>"amcl"</span>, <span class='st'>"nl"</span>) <span class='co'># Amoxicilline met enzymremmer</span>
<span class='fu'>ab_trivial_nl</span>(<span class='st'>"amcl"</span>) <span class='co'># Amoxicilline/clavulaanzuur</span>
<span class='fu'>ab_certe</span>(<span class='st'>"amcl"</span>) <span class='co'># amcl</span>
<span class='fu'>ab_umcg</span>(<span class='st'>"amcl"</span>) <span class='co'># AMCL</span>
<span class='co'># }</span></pre>
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<h1>Name of an antibiotic</h1>
<div class="hidden name"><code>abname.Rd</code></div>
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<div class="ref-description">
<p>Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from <code><a href='antibiotics.html'>antibiotics</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>abname</span>(<span class='no'>abcode</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"guess"</span>, <span class='st'>"atc"</span>, <span class='st'>"certe"</span>, <span class='st'>"umcg"</span>),
<span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"official"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>" + "</span>, <span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>abcode</th>
<td><p>a code or name, like <code>"AMOX"</code>, <code>"AMCL"</code> or <code>"J01CA04"</code></p></td>
</tr>
<tr>
<th>from, to</th>
<td><p>type to transform from and to. See <code><a href='antibiotics.html'>antibiotics</a></code> for its column names. WIth <code>from = "guess"</code> the from will be guessed from <code>"atc"</code>, <code>"certe"</code> and <code>"umcg"</code>. When using <code>to = "atc"</code>, the ATC code will be searched using <code><a href='as.atc.html'>as.atc</a></code>.</p></td>
</tr>
<tr>
<th>textbetween</th>
<td><p>text to put between multiple returned texts</p></td>
</tr>
<tr>
<th>tolower</th>
<td><p>return output as lower case with function <code><a href='https://www.rdocumentation.org/packages/base/topics/chartr'>tolower</a></code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p><code><a href='antibiotics.html'>antibiotics</a></code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>The <code><a href='ab_property.html'>ab_property</a></code> functions are faster and more concise</strong>, but do not support concatenated strings, like <code>abname("AMCL+GENT"</code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>)
<span class='co'># "Amoxicillin and beta-lactamase inhibitor"</span>
<span class='co'># It is quite flexible at default (having `from = "guess"`)</span>
<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"J01CA04"</span>, <span class='st'>"Trimox"</span>, <span class='st'>"dispermox"</span>, <span class='st'>"Amoxil"</span>))
<span class='co'># "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"</span>
<span class='co'># Multiple antibiotics can be combined with "+".</span>
<span class='co'># The second antibiotic will be set to lower case when `tolower` was not set:</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL+GENT"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>"/"</span>)
<span class='co'># "amoxicillin and enzyme inhibitor/gentamicin"</span>
<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMCL"</span>, <span class='st'>"GENT"</span>))
<span class='co'># "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"trivial_nl"</span>)
<span class='co'># "Amoxicilline/clavulaanzuur"</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"atc"</span>)
<span class='co'># "J01CR02"</span>
<span class='co'># specific codes for University Medical Center Groningen (UMCG):</span>
<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"umcg"</span>)
<span class='co'># "AMCL"</span>
<span class='co'># specific codes for Certe:</span>
<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"certe"</span>)
<span class='co'># "amcl"</span>
<span class='co'># }</span></pre>
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<h1>Age in years of individuals</h1>
<div class="hidden name"><code>age.Rd</code></div>
</div>
<div class="ref-description">
<p>Calculates age in years based on a reference date, which is the sytem time at default.</p>
</div>
<pre class="usage"><span class='fu'>age</span>(<span class='no'>x</span>, <span class='kw'>reference</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Sys.time'>Sys.Date</a></span>())</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<th>x</th>
<td><p>date(s), will be coerced with <code><a href='https://www.rdocumentation.org/packages/base/topics/as.POSIXlt'>as.POSIXlt</a></code></p></td>
</tr>
<tr>
<th>reference</th>
<td><p>reference date(s) (defaults to today), will be coerced with <code><a href='https://www.rdocumentation.org/packages/base/topics/as.POSIXlt'>as.POSIXlt</a></code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Integer (no decimals)</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='age_groups.html'>age_groups</a></code> to splits age into groups</p></div>
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<h1>Split ages into age groups</h1>
<div class="hidden name"><code>age_groups.Rd</code></div>
</div>
<div class="ref-description">
<p>Split ages into age groups defined by the <code>split</code> parameter. This allows for easier demographic (antimicrobial resistance) analysis.</p>
</div>
<pre class="usage"><span class='fu'>age_groups</span>(<span class='no'>x</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span>))</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>age, e.g. calculated with <code><a href='age.html'>age</a></code></p></td>
</tr>
<tr>
<th>split_at</th>
<td><p>values to split <code>x</code> at, defaults to age groups 0-11, 12-24, 26-54, 55-74 and 75+. See Details.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered <code><a href='https://www.rdocumentation.org/packages/base/topics/factor'>factor</a></code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>To split ages, the input can be:</p><ul>
<li><p>A numeric vector. A vector of <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(10, 20)</a></code> will split on 0-9, 10-19 and 20+. A value of only <code>50</code> will split on 0-49 and 50+.
The default is to split on young children (0-11), youth (12-24), young adults (26-54), middle-aged adults (55-74) and elderly (75+).</p></li>
<li><p>A character:</p><ul>
<li><p><code>"children"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
<li><p><code>"elderly"</code> or <code>"seniors"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(65, 75, 85, 95)</a></code>. This will split on 0-64, 65-74, 75-84, 85-94 and 95+.</p></li>
<li><p><code>"fives"</code>, equivalent of: <code>1:20 * 5</code>. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.</p></li>
<li><p><code>"tens"</code>, equivalent of: <code>1:10 * 10</code>. This will split on 0-9, 10-19, 20-29 and so forth.</p></li>
</ul></li>
</ul>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='age.html'>age</a></code> to determine ages based on one or more reference dates</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>ages</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
<span class='co'># split into 0-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)
<span class='co'># split into 0-19, 20-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
<span class='co'># split into groups of ten years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)
<span class='co'># split into groups of five years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)
<span class='co'># split specifically for children</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)
<span class='co'># same:</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span></pre>
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<h1>Data set with 423 antibiotics</h1>
<div class="hidden name"><code>antibiotics.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing all antibiotics with a J0 code and some other antimicrobial agents, with their DDDs. Except for trade names and abbreviations, all properties were downloaded from the WHO, see Source.</p>
</div>
<pre class="usage"><span class='no'>antibiotics</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 423 observations and 18 variables:</p><dl class='dl-horizontal'>
<dt><code>atc</code></dt><dd><p>ATC code, like <code>J01CR02</code></p></dd>
<dt><code>certe</code></dt><dd><p>Certe code, like <code>amcl</code></p></dd>
<dt><code>umcg</code></dt><dd><p>UMCG code, like <code>AMCL</code></p></dd>
<dt><code>abbr</code></dt><dd><p>Abbreviation as used by many countries, used internally by <code><a href='as.atc.html'>as.atc</a></code></p></dd>
<dt><code>official</code></dt><dd><p>Official name by the WHO, like <code>"Amoxicillin and beta-lactamase inhibitor"</code></p></dd>
<dt><code>official_nl</code></dt><dd><p>Official name in the Netherlands, like <code>"Amoxicilline met enzymremmer"</code></p></dd>
<dt><code>trivial_nl</code></dt><dd><p>Trivial name in Dutch, like <code>"Amoxicilline/clavulaanzuur"</code></p></dd>
<dt><code>trade_name</code></dt><dd><p>Trade name as used by many countries (a total of 294), used internally by <code><a href='as.atc.html'>as.atc</a></code></p></dd>
<dt><code>oral_ddd</code></dt><dd><p>Defined Daily Dose (DDD), oral treatment</p></dd>
<dt><code>oral_units</code></dt><dd><p>Units of <code>ddd_units</code></p></dd>
<dt><code>iv_ddd</code></dt><dd><p>Defined Daily Dose (DDD), parenteral treatment</p></dd>
<dt><code>iv_units</code></dt><dd><p>Units of <code>iv_ddd</code></p></dd>
<dt><code>atc_group1</code></dt><dd><p>ATC group, like <code>"Macrolides, lincosamides and streptogramins"</code></p></dd>
<dt><code>atc_group2</code></dt><dd><p>Subgroup of <code>atc_group1</code>, like <code>"Macrolides"</code></p></dd>
<dt><code>atc_group1_nl</code></dt><dd><p>ATC group in Dutch, like <code>"Macroliden, lincosamiden en streptograminen"</code></p></dd>
<dt><code>atc_group2_nl</code></dt><dd><p>Subgroup of <code>atc_group1</code> in Dutch, like <code>"Macroliden"</code></p></dd>
<dt><code>useful_gramnegative</code></dt><dd><p><code>FALSE</code> if not useful according to EUCAST, <code>NA</code> otherwise (see Source)</p></dd>
<dt><code>useful_grampositive</code></dt><dd><p><code>FALSE</code> if not useful according to EUCAST, <code>NA</code> otherwise (see Source)</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>- World Health Organization: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a> <br /> - EUCAST - Expert rules intrinsic exceptional V3.1 <br /> - MOLIS (LIS of Certe): <a href='https://www.certe.nl'>https://www.certe.nl</a> <br /> - GLIMS (LIS of UMCG): <a href='https://www.umcg.nl'>https://www.umcg.nl</a></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<h1>Transform to ATC code</h1>
<div class="hidden name"><code>as.atc.Rd</code></div>
</div>
<div class="ref-description">
<p>Use this function to determine the ATC code of one or more antibiotics. The data set <code><a href='antibiotics.html'>antibiotics</a></code> will be searched for abbreviations, official names and trade names.</p>
</div>
<pre class="usage"><span class='fu'>as.atc</span>(<span class='no'>x</span>)
<span class='fu'>guess_atc</span>(<span class='no'>x</span>)
<span class='fu'>is.atc</span>(<span class='no'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>character vector to determine <code>ATC</code> code</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Character (vector) with class <code>"act"</code>. Unknown values will return <code>NA</code>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Use the <code><a href='ab_property.html'>ab_property</a></code> functions to get properties based on the returned ATC code, see Examples.</p>
<p>In the ATC classification system, the active substances are classified in a hierarchy with five different levels. The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups. The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
Source: <a href='https://www.whocc.no/atc/structure_and_principles/'>https://www.whocc.no/atc/structure_and_principles/</a></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='antibiotics.html'>antibiotics</a></code> for the dataframe that is being used to determine ATCs.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># These examples all return "J01FA01", the ATC code of Erythromycin:</span>
<span class='fu'>as.atc</span>(<span class='st'>"J01FA01"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"Erythromycin"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"eryt"</span>)
<span class='fu'>as.atc</span>(<span class='st'>" eryt 123"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"ERYT"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"ERY"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># Trade name</span>
<span class='fu'>as.atc</span>(<span class='st'>"Eryzole"</span>) <span class='co'># Trade name</span>
<span class='fu'>as.atc</span>(<span class='st'>"Pediamycin"</span>) <span class='co'># Trade name</span>
<span class='co'># Use ab_* functions to get a specific property based on an ATC code</span>
<span class='no'>Cipro</span> <span class='kw'>&lt;-</span> <span class='fu'>as.atc</span>(<span class='st'>"cipro"</span>) <span class='co'># returns `J01MA02`</span>
<span class='fu'><a href='ab_property.html'>ab_official</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "Ciprofloxacin"</span>
<span class='fu'><a href='ab_property.html'>ab_umcg</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "CIPR", the code used in the UMCG</span>
<span class='co'># }</span></pre>
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<h1>Class 'mic'</h1>
<div class="hidden name"><code>as.mic.Rd</code></div>
</div>
<div class="ref-description">
<p>This transforms a vector to a new class <code>mic</code>, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as <code>NA</code> with a warning.</p>
</div>
<pre class="usage"><span class='fu'>as.mic</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>is.mic</span>(<span class='no'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>vector</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical indicating whether missing values should be removed</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered factor with new class <code>mic</code></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>mic_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mic</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"&gt;=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"&lt;=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span>))
<span class='fu'>is.mic</span>(<span class='no'>mic_data</span>)
<span class='co'># this can also coerce combined MIC/RSI values:</span>
<span class='fu'>as.mic</span>(<span class='st'>"&lt;=0.002; S"</span>) <span class='co'># will return &lt;=0.002</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>mic_data</span>)
<span class='co'># }</span></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
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<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using Artificial Intelligence (AI) and the complete taxonomic kingdoms Bacteria, Fungi and Protozoa (see Source), so the input can be almost anything: a full name (like &quot;Staphylococcus aureus&quot;), an abbreviated name (like &quot;S. aureus&quot;), an abbreviation known in the field (like &quot;MRSA&quot;), or just a genus. You could also select a genus and species column, zie Examples." />
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<h1>Transform to microorganism ID</h1>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
<div class="ref-description">
<p>Use this function to determine a valid microorganism ID (<code>mo</code>). Determination is done using Artificial Intelligence (AI) and the complete taxonomic kingdoms <em>Bacteria</em>, <em>Fungi</em> and <em>Protozoa</em> (see Source), so the input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (like <code>"S. aureus"</code>), an abbreviation known in the field (like <code>"MRSA"</code>), or just a genus. You could also <code>select</code> a genus and species column, zie Examples.</p>
</div>
<pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>is.mo</span>(<span class='no'>x</span>)
<span class='fu'>guess_mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a character vector or a <code>data.frame</code> with one or two columns</p></td>
</tr>
<tr>
<th>Becker</th>
<td><p>a logical to indicate whether <em>Staphylococci</em> should be categorised into Coagulase Negative <em>Staphylococci</em> ("CoNS") and Coagulase Positive <em>Staphylococci</em> ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> [1].</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></td>
</tr>
<tr>
<th>Lancefield</th>
<td><p>a logical to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These <em>Streptococci</em> 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 <em>Enterococci</em> at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all <em>Enterococci</em> as group D.</p></td>
</tr>
<tr>
<th>allow_uncertain</th>
<td><p>a logical to indicate whether the input should be checked for less possible results, see Details</p></td>
</tr>
<tr>
<th>reference_df</th>
<td><p>a <code>data.frame</code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. The first column can be any microbial name, code or ID (used in your analysis or organisation), the second column must be a valid <code>mo</code> as found in the <code><a href='microorganisms.html'>microorganisms</a></code> data set.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Character (vector) with class <code>"mo"</code>. Unknown values will return <code>NA</code>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>A microbial ID from this package (class: <code>mo</code>) typically looks like these examples:<br /></p><pre>
Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNE Klebsiella pneumoniae
B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ----&gt; subspecies, a 3-4 letter acronym
| | ----&gt; species, a 3-4 letter acronym
| ----&gt; genus, a 5-7 letter acronym, mostly without vowels
----&gt; taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
</pre>
<p>Use the <code><a href='mo_property.html'>mo_property</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:</p><ul>
<li><p>Taxonomic kingdom: it first searches in bacteria, then fungi, then protozoa</p></li>
<li><p>Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones</p></li>
<li><p>Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations</p></li>
<li><p>Breakdown of input values: from here it starts to breakdown input values to find possible matches</p></li>
</ul>
<p>A couple of effects because of these rules:</p><ul>
<li><p><code>"E. coli"</code> will return the ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em>, although the latter would alphabetically come first</p></li>
<li><p><code>"H. influenzae"</code> will return the ID of <em>Haemophilus influenzae</em> and not <em>Haematobacter influenzae</em> for the same reason</p></li>
<li><p>Something like <code>"p aer"</code> will return the ID of <em>Pseudomonas aeruginosa</em> and not <em>Pasteurella aerogenes</em></p></li>
<li><p>Something like <code>"stau"</code> or <code>"S aur"</code> will return the ID of <em>Staphylococcus aureus</em> and not <em>Staphylococcus auricularis</em></p></li>
</ul><p>This means that looking up human pathogenic microorganisms takes less time than looking up human <strong>non</strong>-pathogenic microorganisms.</p>
<p>When using <code>allow_uncertain = TRUE</code> (which is the default setting), it will use additional rules if all previous AI rules failed to get valid results. Examples:</p><ul>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPTC_GRB</code>) needs review.</p></li>
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
<li><p><code>"D. spartina"</code>. This is the abbreviation of an old taxonomic name: <em>Didymosphaeria spartinae</em> (the last "e" was missing from the input). This fungus was renamed to <em>Leptosphaeria obiones</em>, so a warning will be thrown that this result (<code>F_LPTSP_OBI</code>) needs review.</p></li>
</ul>
<p><code>guess_mo</code> is an alias of <code>as.mo</code>.</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<p><img src='figures/itis_logo.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
<p>[2] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
<p>[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. <a href='http://www.itis.gov'>http://www.itis.gov</a></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='microorganisms.html'>microorganisms</a></code> for the <code>data.frame</code> with ITIS content that is being used to determine ID's. <br />
The <code><a href='mo_property.html'>mo_property</a></code> functions (like <code><a href='mo_property.html'>mo_genus</a></code>, <code><a href='mo_property.html'>mo_gramstain</a></code>) to get properties based on the returned code.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># These examples all return "B_STPHY_AUR", the ID of S. aureus:</span>
<span class='fu'>as.mo</span>(<span class='st'>"stau"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"STAU"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"staaur"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"S. aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"S aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='fl'>369</span>) <span class='co'># Search on TSN (Taxonomic Serial Number), a unique identifier</span>
<span class='co'># for the Integrated Taxonomic Information System (ITIS)</span>
<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
<span class='co'># guess_mo is an alias of as.mo and works the same</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CNS</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPTC_GRA</span>
<span class='co'># Use mo_* functions to get a specific property based on `mo`</span>
<span class='no'>Ecoli</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='st'>"E. coli"</span>) <span class='co'># returns `B_ESCHR_COL`</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>Ecoli</span>) <span class='co'># returns "Escherichia"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='no'>Ecoli</span>) <span class='co'># returns "Gram negative"</span>
<span class='co'># but it uses as.mo internally too, so you could also just use:</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='no'>df</span>$<span class='no'>microorganism_name</span>)
<span class='co'># the select function of tidyverse is also supported:</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># although this works easier and does the same:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
<span class='co'># }</span></pre>
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<h1>Class 'rsi'</h1>
<div class="hidden name"><code>as.rsi.Rd</code></div>
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<div class="ref-description">
<p>This transforms a vector to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
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<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>)
<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<th>x</th>
<td><p>vector</p></td>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered factor with new class <code>rsi</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>is.rsi.eligible</code> returns <code>TRUE</code> when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and <code>FALSE</code> otherwise.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>rsi_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
<span class='no'>rsi_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>), <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span>))
<span class='fu'>is.rsi</span>(<span class='no'>rsi_data</span>)
<span class='co'># this can also coerce combined MIC/RSI values:</span>
<span class='fu'>as.rsi</span>(<span class='st'>"&lt;= 0.002; S"</span>) <span class='co'># will return S</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span>
<span class='co'># using dplyr's mutate</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='http://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
<span class='no'>as.rsi</span>)
<span class='co'># }</span></pre>
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<h1>Properties of an ATC code</h1>
<div class="hidden name"><code>atc_property.Rd</code></div>
</div>
<div class="ref-description">
<p>Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. <br /> <strong>This function requires an internet connection.</strong></p>
</div>
<pre class="usage"><span class='fu'>atc_property</span>(<span class='no'>atc_code</span>, <span class='no'>property</span>, <span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"O"</span>,
<span class='kw'>url</span> <span class='kw'>=</span> <span class='st'>"https://www.whocc.no/atc_ddd_index/?code=%s&amp;showdescription=no"</span>)
<span class='fu'>atc_groups</span>(<span class='no'>atc_code</span>, <span class='no'>...</span>)
<span class='fu'>atc_ddd</span>(<span class='no'>atc_code</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>atc_code</th>
<td><p>a character or character vector with ATC code(s) of antibiotic(s)</p></td>
</tr>
<tr>
<th>property</th>
<td><p>property of an ATC code. Valid values are <code>"ATC"</code>, <code>"Name"</code>, <code>"DDD"</code>, <code>"U"</code> (<code>"unit"</code>), <code>"Adm.R"</code>, <code>"Note"</code> and <code>groups</code>. For this last option, all hierarchical groups of an ATC code will be returned, see Examples.</p></td>
</tr>
<tr>
<th>administration</th>
<td><p>type of administration when using <code>property = "Adm.R"</code>, see Details</p></td>
</tr>
<tr>
<th>url</th>
<td><p>url of website of the WHO. The sign <code>%s</code> can be used as a placeholder for ATC codes.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>parameters to pass on to <code>atc_property</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p><a href='https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/'>https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/</a></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Options for parameter <code>administration</code>:</p><ul>
<li><p><code>"Implant"</code> = Implant</p></li>
<li><p><code>"Inhal"</code> = Inhalation</p></li>
<li><p><code>"Instill"</code> = Instillation</p></li>
<li><p><code>"N"</code> = nasal</p></li>
<li><p><code>"O"</code> = oral</p></li>
<li><p><code>"P"</code> = parenteral</p></li>
<li><p><code>"R"</code> = rectal</p></li>
<li><p><code>"SL"</code> = sublingual/buccal</p></li>
<li><p><code>"TD"</code> = transdermal</p></li>
<li><p><code>"V"</code> = vaginal</p></li>
</ul>
<p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul>
<li><p><code>"g"</code> = gram</p></li>
<li><p><code>"mg"</code> = milligram</p></li>
<li><p><code>"mcg"</code> = microgram</p></li>
<li><p><code>"U"</code> = unit</p></li>
<li><p><code>"TU"</code> = thousand units</p></li>
<li><p><code>"MU"</code> = million units</p></li>
<li><p><code>"mmol"</code> = millimole</p></li>
<li><p><code>"ml"</code> = milliliter (e.g. eyedrops)</p></li>
</ul>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># What's the ATC of amoxicillin?</span>
<span class='fu'><a href='as.atc.html'>guess_atc</a></span>(<span class='st'>"Amoxicillin"</span>)
<span class='co'># [1] "J01CA04"</span>
<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
<span class='fu'>atc_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span>)
<span class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
<span class='fu'>atc_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span>)
<span class='fu'>atc_property</span>(<span class='st'>"J01CA04"</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"groups"</span>) <span class='co'># search hierarchical groups of amoxicillin</span>
<span class='co'># [1] "ANTIINFECTIVES FOR SYSTEMIC USE"</span>
<span class='co'># [2] "ANTIBACTERIALS FOR SYSTEMIC USE"</span>
<span class='co'># [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
<span class='co'># [4] "Penicillins with extended spectrum"</span>
<span class='co'># }</span></pre>
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<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
count_R and count_IR can be used to count resistant isolates, count_S and count_SI can be used to count susceptible isolates." />
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<h1>Count isolates</h1>
<div class="hidden name"><code>count.Rd</code></div>
</div>
<div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>count_R</code> and <code>count_IR</code> can be used to count resistant isolates, <code>count_S</code> and <code>count_SI</code> can be used to count susceptible isolates.<br /></p>
</div>
<pre class="usage"><span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_IR</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_I</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_SI</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_S</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_all</span>(<span class='no'>...</span>)
<span class='fu'>n_rsi</span>(<span class='no'>...</span>)
<span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"get_antibiotic_names"</span>,
<span class='st'>"official"</span>), <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>...</th>
<td><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href='as.rsi.html'>as.rsi</a></code> if needed.</p></td>
</tr>
<tr>
<th>also_single_tested</th>
<td><p>a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of <code>portion_S</code> and R in case of <code>portion_R</code>). <strong>This would lead to selection bias in almost all cases.</strong></p></td>
</tr>
<tr>
<th>data</th>
<td><p>a <code>data.frame</code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='abname.html'>abname</a></code>. This can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("get_antibiotic_names")</code>.</p></td>
</tr>
<tr>
<th>combine_IR</th>
<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Wickham H. <strong>Tidy Data.</strong> The Journal of Statistical Software, vol. 59, 2014. <a href='http://vita.had.co.nz/papers/tidy-data.html'>http://vita.had.co.nz/papers/tidy-data.html</a></p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Integer</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='http://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='portion.html'>portion</a>_*</code> to calculate microbial resistance and susceptibility.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a data set available in the AMR package. It is true, genuine data.</span>
?<span class='no'>septic_patients</span>
<span class='co'># Count resistant isolates</span>
<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Or susceptible isolates</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Count all available isolates</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Since n_rsi counts available isolates, you can</span>
<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
<span class='co'># This results in the same:</span>
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1057 (67.1%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1576</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># S = 1372 (74.0%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># n = 1855</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1396 (92.0%)</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1517</span>
<span class='fu'>n_rsi</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>))
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># }</span></pre>
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<h1>EUCAST rules</h1>
<div class="hidden name"><code>eucast_rules.Rd</code></div>
</div>
<div class="ref-description">
<p>Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='http://eucast.org'>http://eucast.org</a>), see <em>Source</em>. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.</p>
</div>
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>amik</span> <span class='kw'>=</span> <span class='st'>"amik"</span>, <span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='st'>"ampi"</span>,
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='st'>"azit"</span>, <span class='kw'>azlo</span> <span class='kw'>=</span> <span class='st'>"azlo"</span>, <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='st'>"aztr"</span>, <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='st'>"cefa"</span>,
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='st'>"cfep"</span>, <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>, <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"cfox"</span>, <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='st'>"cfra"</span>,
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='st'>"cftr"</span>, <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='st'>"chlo"</span>,
<span class='kw'>cipr</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>clar</span> <span class='kw'>=</span> <span class='st'>"clar"</span>, <span class='kw'>clin</span> <span class='kw'>=</span> <span class='st'>"clin"</span>, <span class='kw'>clox</span> <span class='kw'>=</span> <span class='st'>"clox"</span>,
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>czol</span> <span class='kw'>=</span> <span class='st'>"czol"</span>, <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='st'>"dapt"</span>, <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='st'>"doxy"</span>,
<span class='kw'>erta</span> <span class='kw'>=</span> <span class='st'>"erta"</span>, <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>, <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='st'>"fosf"</span>, <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='st'>"fusi"</span>,
<span class='kw'>gent</span> <span class='kw'>=</span> <span class='st'>"gent"</span>, <span class='kw'>imip</span> <span class='kw'>=</span> <span class='st'>"imip"</span>, <span class='kw'>kana</span> <span class='kw'>=</span> <span class='st'>"kana"</span>, <span class='kw'>levo</span> <span class='kw'>=</span> <span class='st'>"levo"</span>,
<span class='kw'>linc</span> <span class='kw'>=</span> <span class='st'>"linc"</span>, <span class='kw'>line</span> <span class='kw'>=</span> <span class='st'>"line"</span>, <span class='kw'>mero</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>mezl</span> <span class='kw'>=</span> <span class='st'>"mezl"</span>,
<span class='kw'>mino</span> <span class='kw'>=</span> <span class='st'>"mino"</span>, <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='st'>"moxi"</span>, <span class='kw'>nali</span> <span class='kw'>=</span> <span class='st'>"nali"</span>, <span class='kw'>neom</span> <span class='kw'>=</span> <span class='st'>"neom"</span>,
<span class='kw'>neti</span> <span class='kw'>=</span> <span class='st'>"neti"</span>, <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='st'>"nitr"</span>, <span class='kw'>norf</span> <span class='kw'>=</span> <span class='st'>"norf"</span>, <span class='kw'>novo</span> <span class='kw'>=</span> <span class='st'>"novo"</span>,
<span class='kw'>oflo</span> <span class='kw'>=</span> <span class='st'>"oflo"</span>, <span class='kw'>oxac</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"peni"</span>, <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='st'>"pipe"</span>,
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='st'>"pita"</span>, <span class='kw'>poly</span> <span class='kw'>=</span> <span class='st'>"poly"</span>, <span class='kw'>pris</span> <span class='kw'>=</span> <span class='st'>"pris"</span>, <span class='kw'>qida</span> <span class='kw'>=</span> <span class='st'>"qida"</span>,
<span class='kw'>rifa</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='st'>"roxi"</span>, <span class='kw'>siso</span> <span class='kw'>=</span> <span class='st'>"siso"</span>, <span class='kw'>teic</span> <span class='kw'>=</span> <span class='st'>"teic"</span>,
<span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>tica</span> <span class='kw'>=</span> <span class='st'>"tica"</span>, <span class='kw'>tige</span> <span class='kw'>=</span> <span class='st'>"tige"</span>, <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>,
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='st'>"trim"</span>, <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>)
<span class='fu'>EUCAST_rules</span>(<span class='no'>...</span>)
<span class='fu'>interpretive_reading</span>(<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tbl</th>
<td><p>table with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td>
</tr>
<tr>
<th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr>
<tr>
<th>info</th>
<td><p>print progress</p></td>
</tr>
<tr>
<th>rules</th>
<td><p>a character vector that specifies which rules should be applied - one or more of <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c("breakpoints", "expert", "other", "all")</a></code></p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected</p></td>
</tr>
<tr>
<th>amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>...</th>
<td><p>parameters that are passed on to <code>eucast_rules</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<ul>
<li><p>EUCAST Expert Rules. Version 2.0, 2012. <br />
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <br />
<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx</a></p></li>
</ul>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with verbose info.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
<p>To define antibiotics column names, input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>),
<strong>amox</strong>: amoxicillin (<em>J01CA04</em>),
<strong>ampi</strong>: ampicillin (<em>J01CA01</em>),
<strong>azit</strong>: azithromycin (<em>J01FA10</em>),
<strong>azlo</strong>: azlocillin (<em>J01CA09</em>),
<strong>aztr</strong>: aztreonam (<em>J01DF01</em>),
<strong>cefa</strong>: cefaloridine (<em>J01DB02</em>),
<strong>cfep</strong>: cefepime (<em>J01DE01</em>),
<strong>cfot</strong>: cefotaxime (<em>J01DD01</em>),
<strong>cfox</strong>: cefoxitin (<em>J01DC01</em>),
<strong>cfra</strong>: cefradine (<em>J01DB09</em>),
<strong>cfta</strong>: ceftazidime (<em>J01DD02</em>),
<strong>cftr</strong>: ceftriaxone (<em>J01DD04</em>),
<strong>cfur</strong>: cefuroxime (<em>J01DC02</em>),
<strong>chlo</strong>: chloramphenicol (<em>J01BA01</em>),
<strong>cipr</strong>: ciprofloxacin (<em>J01MA02</em>),
<strong>clar</strong>: clarithromycin (<em>J01FA09</em>),
<strong>clin</strong>: clindamycin (<em>J01FF01</em>),
<strong>clox</strong>: flucloxacillin (<em>J01CF05</em>),
<strong>coli</strong>: colistin (<em>J01XB01</em>),
<strong>czol</strong>: cefazolin (<em>J01DB04</em>),
<strong>dapt</strong>: daptomycin (<em>J01XX09</em>),
<strong>doxy</strong>: doxycycline (<em>J01AA02</em>),
<strong>erta</strong>: ertapenem (<em>J01DH03</em>),
<strong>eryt</strong>: erythromycin (<em>J01FA01</em>),
<strong>fosf</strong>: fosfomycin (<em>J01XX01</em>),
<strong>fusi</strong>: fusidic acid (<em>J01XC01</em>),
<strong>gent</strong>: gentamicin (<em>J01GB03</em>),
<strong>imip</strong>: imipenem (<em>J01DH51</em>),
<strong>kana</strong>: kanamycin (<em>J01GB04</em>),
<strong>levo</strong>: levofloxacin (<em>J01MA12</em>),
<strong>linc</strong>: lincomycin (<em>J01FF02</em>),
<strong>line</strong>: linezolid (<em>J01XX08</em>),
<strong>mero</strong>: meropenem (<em>J01DH02</em>),
<strong>mezl</strong>: mezlocillin (<em>J01CA10</em>),
<strong>mino</strong>: minocycline (<em>J01AA08</em>),
<strong>moxi</strong>: moxifloxacin (<em>J01MA14</em>),
<strong>nali</strong>: nalidixic acid (<em>J01MB02</em>),
<strong>neom</strong>: neomycin (<em>J01GB05</em>),
<strong>neti</strong>: netilmicin (<em>J01GB07</em>),
<strong>nitr</strong>: nitrofurantoin (<em>J01XE01</em>),
<strong>norf</strong>: norfloxacin (<em>J01MA06</em>),
<strong>novo</strong>: novobiocin (an ATCvet code: <em>QJ01XX95</em>),
<strong>oflo</strong>: ofloxacin (<em>J01MA01</em>),
<strong>peni</strong>: penicillin (<em>J01RA01</em>),
<strong>pipe</strong>: piperacillin (<em>J01CA12</em>),
<strong>pita</strong>: piperacillin+tazobactam (<em>J01CR05</em>),
<strong>poly</strong>: polymyxin B (<em>J01XB02</em>),
<strong>pris</strong>: pristinamycin (<em>J01FG01</em>),
<strong>qida</strong>: quinupristin/dalfopristin (<em>J01FG02</em>),
<strong>rifa</strong>: rifampicin (<em>J04AB02</em>),
<strong>roxi</strong>: roxithromycin (<em>J01FA06</em>),
<strong>siso</strong>: sisomicin (<em>J01GB08</em>),
<strong>teic</strong>: teicoplanin (<em>J01XA02</em>),
<strong>tetr</strong>: tetracycline (<em>J01AA07</em>),
<strong>tica</strong>: ticarcillin (<em>J01CA13</em>),
<strong>tige</strong>: tigecycline (<em>J01AA12</em>),
<strong>tobr</strong>: tobramycin (<em>J01GB01</em>),
<strong>trim</strong>: trimethoprim (<em>J01EA01</em>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>),
<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
<span class='st'>"Klebsiella pneumoniae"</span>,
<span class='st'>"Pseudomonas aeruginosa"</span>),
<span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
<span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
<span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
<span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='no'>a</span>
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
<span class='co'># 3 Escherichia coli - - - - - S S</span>
<span class='co'># 4 Klebsiella pneumoniae - - - - - S S</span>
<span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='st'>"mo"</span>) <span class='co'># 18 results are forced as R or S</span>
<span class='no'>b</span>
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
<span class='co'># 3 Escherichia coli R - - - - R S</span>
<span class='co'># 4 Klebsiella pneumoniae R R - - - R S</span>
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
<span class='co'># }</span></pre>
</div>
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<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#examples">Examples</a></li>
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<h1>Determine first (weighted) isolates</h1>
<div class="hidden name"><code>first_isolate.Rd</code></div>
</div>
<div class="ref-description">
<p>Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.</p>
</div>
<pre class="usage"><span class='fu'>first_isolate</span>(<span class='no'>tbl</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_testcode</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_specimen</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_icu</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>episode_days</span> <span class='kw'>=</span> <span class='fl'>365</span>,
<span class='kw'>testcodes_exclude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>icu_exclude</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"keyantibiotics"</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='fu'>filter_first_isolate</span>(<span class='no'>tbl</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
<span class='fu'>filter_first_weighted_isolate</span>(<span class='no'>tbl</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tbl</th>
<td><p>a <code>data.frame</code> containing isolates.</p></td>
</tr>
<tr>
<th>col_date</th>
<td><p>column name of the result date (or date that is was received on the lab), defaults to the first column of class <code>Date</code></p></td>
</tr>
<tr>
<th>col_patient_id</th>
<td><p>column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)</p></td>
</tr>
<tr>
<th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr>
<tr>
<th>col_testcode</th>
<td><p>column name of the test codes. Use <code>col_testcode = NULL</code> to <strong>not</strong> exclude certain test codes (like test codes for screening). In that case <code>testcodes_exclude</code> will be ignored.</p></td>
</tr>
<tr>
<th>col_specimen</th>
<td><p>column name of the specimen type or group</p></td>
</tr>
<tr>
<th>col_icu</th>
<td><p>column name of the logicals (<code>TRUE</code>/<code>FALSE</code>) whether a ward or department is an Intensive Care Unit (ICU)</p></td>
</tr>
<tr>
<th>col_keyantibiotics</th>
<td><p>column name of the key antibiotics to determine first <em>weighted</em> isolates, see <code><a href='key_antibiotics.html'>key_antibiotics</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use <code>col_keyantibiotics = FALSE</code> to prevent this.</p></td>
</tr>
<tr>
<th>episode_days</th>
<td><p>episode in days after which a genus/species combination will be determined as 'first isolate' again</p></td>
</tr>
<tr>
<th>testcodes_exclude</th>
<td><p>character vector with test codes that should be excluded (case-insensitive)</p></td>
</tr>
<tr>
<th>icu_exclude</th>
<td><p>logical whether ICU isolates should be excluded (rows with value <code>TRUE</code> in column <code>col_icu</code>)</p></td>
</tr>
<tr>
<th>specimen_group</th>
<td><p>value in column <code>col_specimen</code> to filter on</p></td>
</tr>
<tr>
<th>type</th>
<td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see Details</p></td>
</tr>
<tr>
<th>ignore_I</th>
<td><p>logical to determine whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see Details</p></td>
</tr>
<tr>
<th>points_threshold</th>
<td><p>points until the comparison of key antibiotics will lead to inclusion of an isolate when <code>type = "points"</code>, see Details</p></td>
</tr>
<tr>
<th>info</th>
<td><p>print progress</p></td>
</tr>
<tr>
<th>...</th>
<td><p>parameters passed on to the <code>first_isolate</code> function</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Methodology of this function is based on: <strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Logical vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode <a href='https://www.ncbi.nlm.nih.gov/pubmed/17304462'>[1]</a>. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all <em>S. aureus</em> isolates would be overestimated, because you included this MRSA more than once. It would be <a href='https://en.wikipedia.org/wiki/Selection_bias'>selection bias</a>.</p>
<p>The function <code>filter_first_isolate</code> is essentially equal to:</p><pre>
tbl %&gt;%
mutate(only_firsts = first_isolate(tbl, ...)) %&gt;%
filter(only_firsts == TRUE) %&gt;%
select(-only_firsts)
</pre><p>The function <code>filter_first_weighted_isolate</code> is essentially equal to:</p><pre>
tbl %&gt;%
mutate(keyab = key_antibiotics(.)) %&gt;%
mutate(only_weighted_firsts = first_isolate(tbl,
col_keyantibiotics = "keyab", ...)) %&gt;%
filter(only_weighted_firsts == TRUE) %&gt;%
select(-only_weighted_firsts)
</pre>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
<p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results: <br /></p>
<p><strong>1. Using</strong> <code>type = "keyantibiotics"</code> <strong>and parameter</strong> <code>ignore_I</code> <br />
Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. <br /></p>
<p><strong>2. Using</strong> <code>type = "points"</code> <strong>and parameter</strong> <code>points_threshold</code> <br />
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, an isolate will be (re)selected as a first weighted isolate.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a dataset available in the AMR package. It is true, genuine data.</span>
?<span class='no'>septic_patients</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># Filter on first isolates:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
<span class='co'># Which can be shortened to:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_isolate</span>()
<span class='co'># or for first weighted isolates:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>()
<span class='co'># Now let's see if first isolates matter:</span>
<span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
<span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
<span class='co'># Have a look at A and B.</span>
<span class='co'># B is more reliable because every isolate is only counted once.</span>
<span class='co'># Gentamicin resitance in hospital D appears to be 5.4% higher than</span>
<span class='co'># when you (erroneously) would have used all isolates!</span>
<span class='co'>## OTHER EXAMPLES:</span>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>tbl</span>$<span class='no'>keyab</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>tbl</span>)
<span class='no'>tbl</span>$<span class='no'>first_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>)
<span class='no'>tbl</span>$<span class='no'>first_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>tbl</span>$<span class='no'>first_blood_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Blood'</span>)
<span class='no'>tbl</span>$<span class='no'>first_blood_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Blood'</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>tbl</span>$<span class='no'>first_urine_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Urine'</span>)
<span class='no'>tbl</span>$<span class='no'>first_urine_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Urine'</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>tbl</span>$<span class='no'>first_resp_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Respiratory'</span>)
<span class='no'>tbl</span>$<span class='no'>first_resp_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Respiratory'</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='co'># }</span></pre>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#key-antibiotics">Key antibiotics</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
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<h1>Frequency table</h1>
<div class="hidden name"><code>freq.Rd</code></div>
</div>
<div class="ref-description">
<p>Create a frequency table of a vector with items or a data frame. Supports quasiquotation and markdown for reports. <code>top_freq</code> can be used to get the top/bottom <em>n</em> items of a frequency table, with counts as names.</p>
</div>
<pre class="usage"><span class='fu'>frequency_tbl</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>header</span> <span class='kw'>=</span> !<span class='no'>markdown</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>na</span> <span class='kw'>=</span> <span class='st'>"&lt;NA&gt;"</span>, <span class='kw'>droplevels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" "</span>, <span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>),
<span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span> <span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>))
<span class='fu'>freq</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>),
<span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(),
<span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>header</span> <span class='kw'>=</span> !<span class='no'>markdown</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>na</span> <span class='kw'>=</span> <span class='st'>"&lt;NA&gt;"</span>, <span class='kw'>droplevels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" "</span>,
<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span>
<span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>))
<span class='fu'>top_freq</span>(<span class='no'>f</span>, <span class='no'>n</span>)
<span class='fu'>header</span>(<span class='no'>f</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='co'># S3 method for frequency_tbl</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>,
<span class='kw'>default</span> <span class='kw'>=</span> <span class='fl'>15</span>), <span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>header</span> <span class='kw'>=</span> !<span class='no'>markdown</span>,
<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span>
<span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>), <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>vector of any class or a <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code>, <code>tibble</code> (may contain a grouping variable) or <code><a href='https://www.rdocumentation.org/packages/base/topics/table'>table</a></code></p></td>
</tr>
<tr>
<th>...</th>
<td><p>up to nine different columns of <code>x</code> when <code>x</code> is a <code>data.frame</code> or <code>tibble</code>, to calculate frequencies from - see Examples</p></td>
</tr>
<tr>
<th>sort.count</th>
<td><p>sort on count, i.e. frequencies. This will be <code>TRUE</code> at default for everything except when using grouping variables.</p></td>
</tr>
<tr>
<th>nmax</th>
<td><p>number of row to print. The default, <code>15</code>, uses <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("max.print.freq")</code>. Use <code>nmax = 0</code>, <code>nmax = Inf</code>, <code>nmax = NULL</code> or <code>nmax = NA</code> to print all rows.</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical value indicating whether <code>NA</code> values should be removed from the frequency table. The header (if set) will always print the amount of <code>NA</code>s.</p></td>
</tr>
<tr>
<th>row.names</th>
<td><p>a logical value indicating whether row indices should be printed as <code>1:nrow(x)</code></p></td>
</tr>
<tr>
<th>markdown</th>
<td><p>a logical value indicating whether the frequency table should be printed in markdown format. This will print all rows (except when <code>nmax</code> is defined) and is default behaviour in non-interactive R sessions (like when knitting RMarkdown files).</p></td>
</tr>
<tr>
<th>digits</th>
<td><p>how many significant digits are to be used for numeric values in the header (not for the items themselves, that depends on <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("digits")</code>)</p></td>
</tr>
<tr>
<th>quote</th>
<td><p>a logical value indicating whether or not strings should be printed with surrounding quotes</p></td>
</tr>
<tr>
<th>header</th>
<td><p>a logical value indicating whether an informative header should be printed</p></td>
</tr>
<tr>
<th>title</th>
<td><p>text to show above frequency table, at default to tries to coerce from the variables passed to <code>x</code></p></td>
</tr>
<tr>
<th>na</th>
<td><p>a character string to should be used to show empty (<code>NA</code>) values (only useful when <code>na.rm = FALSE</code>)</p></td>
</tr>
<tr>
<th>droplevels</th>
<td><p>a logical value indicating whether in factors empty levels should be dropped</p></td>
</tr>
<tr>
<th>sep</th>
<td><p>a character string to separate the terms when selecting multiple columns</p></td>
</tr>
<tr>
<th>decimal.mark</th>
<td><p><!-- % -->
used for prettying (longish) numerical and complex sequences.
Passed to <code><a href='https://www.rdocumentation.org/packages/base/topics/formatc'>prettyNum</a></code>: that help page explains the details.</p></td>
</tr>
<tr>
<th>big.mark</th>
<td><p><!-- % -->
used for prettying (longish) numerical and complex sequences.
Passed to <code><a href='https://www.rdocumentation.org/packages/base/topics/formatc'>prettyNum</a></code>: that help page explains the details.</p></td>
</tr>
<tr>
<th>f</th>
<td><p>a frequency table</p></td>
</tr>
<tr>
<th>n</th>
<td><p>number of top <em>n</em> items to return, use -n for the bottom <em>n</em> items. It will include more than <code>n</code> rows if there are ties.</p></td>
</tr>
<tr>
<th>property</th>
<td><p>property in header to return this value directly</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A <code>data.frame</code> (with an additional class <code>"frequency_tbl"</code>) with five columns: <code>item</code>, <code>count</code>, <code>percent</code>, <code>cum_count</code> and <code>cum_percent</code>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the `freq` function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. This package also has a vignette available to explain the use of this function further, run <code><a href='https://www.rdocumentation.org/packages/utils/topics/browseVignettes'>browseVignettes("AMR")</a></code> to read it.</p>
<p>For numeric values of any class, these additional values will all be calculated with <code>na.rm = TRUE</code> and shown into the header:</p><ul>
<li><p>Mean, using <code><a href='https://www.rdocumentation.org/packages/base/topics/mean'>mean</a></code></p></li>
<li><p>Standard Deviation, using <code><a href='https://www.rdocumentation.org/packages/stats/topics/sd'>sd</a></code></p></li>
<li><p>Coefficient of Variation (CV), the standard deviation divided by the mean</p></li>
<li><p>Mean Absolute Deviation (MAD), using <code><a href='https://www.rdocumentation.org/packages/stats/topics/mad'>mad</a></code></p></li>
<li><p>Tukey Five-Number Summaries (minimum, Q1, median, Q3, maximum), using <code><a href='https://www.rdocumentation.org/packages/stats/topics/fivenum'>fivenum</a></code></p></li>
<li><p>Interquartile Range (IQR) calculated as <code>Q3 - Q1</code> using the Tukey Five-Number Summaries, i.e. <strong>not</strong> using the <code><a href='https://www.rdocumentation.org/packages/stats/topics/quantile'>quantile</a></code> function</p></li>
<li><p>Coefficient of Quartile Variation (CQV, sometimes called coefficient of dispersion), calculated as <code>(Q3 - Q1) / (Q3 + Q1)</code> using the Tukey Five-Number Summaries</p></li>
<li><p>Outliers (total count and unique count), using <code><a href='https://www.rdocumentation.org/packages/grDevices/topics/boxplot.stats'>boxplot.stats</a></code></p></li>
</ul>
<p>For dates and times of any class, these additional values will be calculated with <code>na.rm = TRUE</code> and shown into the header:</p><ul>
<li><p>Oldest, using <code><a href='https://www.rdocumentation.org/packages/base/topics/Extremes'>min</a></code></p></li>
<li><p>Newest, using <code><a href='https://www.rdocumentation.org/packages/base/topics/Extremes'>max</a></code>, with difference between newest and oldest</p></li>
<li><p>Median, using <code><a href='https://www.rdocumentation.org/packages/stats/topics/median'>median</a></code>, with percentage since oldest</p></li>
</ul>
<p>In factors, all factor levels that are not existing in the input data will be dropped.</p>
<p>The function <code>top_freq</code> uses <code><a href='http://dplyr.tidyverse.org/reference/top_n.html'>top_n</a></code> internally and will include more than <code>n</code> rows if there are ties.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># this all gives the same result:</span>
<span class='fu'>freq</span>(<span class='no'>septic_patients</span>$<span class='no'>hospital_id</span>)
<span class='fu'>freq</span>(<span class='no'>septic_patients</span>[, <span class='st'>"hospital_id"</span>])
<span class='no'>septic_patients</span>$<span class='no'>hospital_id</span> <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>()
<span class='no'>septic_patients</span>[, <span class='st'>"hospital_id"</span>] <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>()
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>(<span class='st'>"hospital_id"</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='co'>#&lt;- easiest to remember (tidyverse)</span>
<span class='co'># you could also use `select` or `pull` to get your variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>()
<span class='co'># multiple selected variables will be pasted together</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='no'>left_join_microorganisms</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>genus</span>, <span class='no'>species</span>)
<span class='co'># group a variable and analyse another</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>gender</span>)
<span class='co'># get top 10 bugs of hospital A as a vector</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>top_freq</span>(<span class='fl'>10</span>)
<span class='co'># save frequency table to an object</span>
<span class='no'>years</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>year</span>)
<span class='co'># show only the top 5</span>
<span class='no'>years</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fl'>5</span>)
<span class='co'># save to an object with formatted percentages</span>
<span class='no'>years</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>years</span>)
<span class='co'># print a histogram of numeric values</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/hist'>hist</a></span>()
<span class='co'># or print all points to a regular plot</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>()
<span class='co'># transform to a data.frame or tibble</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/as.data.frame'>as.data.frame</a></span>()
<span class='co'># or transform (back) to a vector</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/vector'>as.vector</a></span>()
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/identical'>identical</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/vector'>as.vector</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sort'>sort</a></span>(),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sort'>sort</a></span>(<span class='no'>septic_patients</span>$<span class='no'>age</span>)) <span class='co'># TRUE</span>
<span class='co'># it also supports `table` objects</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/table'>table</a></span>(<span class='no'>septic_patients</span>$<span class='no'>gender</span>,
<span class='no'>septic_patients</span>$<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" **sep** "</span>)
<span class='co'># only get selected columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
<span class='co'># check differences between frequency tables</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/diff'>diff</a></span>(<span class='fu'>freq</span>(<span class='no'>septic_patients</span>$<span class='no'>trim</span>),
<span class='fu'>freq</span>(<span class='no'>septic_patients</span>$<span class='no'>trsu</span>))
<span class='co'># }</span></pre>
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<h1><em>G</em>-test for Count Data</h1>
<div class="hidden name"><code>g.test.Rd</code></div>
</div>
<div class="ref-description">
<p><code>g.test</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href='https://www.rdocumentation.org/packages/stats/topics/chisq.test'>chisq.test</a></code> but is more reliable [1]. A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
</div>
<pre class="usage"><span class='fu'>g.test</span>(<span class='no'>x</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='fl'>1</span>/<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/length'>length</a></span>(<span class='no'>x</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/length'>length</a></span>(<span class='no'>x</span>)),
<span class='kw'>rescale.p</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a numeric vector or matrix. <code>x</code> and <code>y</code> can also
both be factors.</p></td>
</tr>
<tr>
<th>y</th>
<td><p>a numeric vector; ignored if <code>x</code> is a matrix. If
<code>x</code> is a factor, <code>y</code> should be a factor of the same length.</p></td>
</tr>
<tr>
<th>p</th>
<td><p>a vector of probabilities of the same length of <code>x</code>.
An error is given if any entry of <code>p</code> is negative.</p></td>
</tr>
<tr>
<th>rescale.p</th>
<td><p>a logical scalar; if TRUE then <code>p</code> is rescaled
(if necessary) to sum to 1. If <code>rescale.p</code> is FALSE, and
<code>p</code> does not sum to 1, an error is given.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>This code is almost identical to <code><a href='https://www.rdocumentation.org/packages/stats/topics/chisq.test'>chisq.test</a></code>, except that:</p><ul>
<li><p>The calculation of the statistic was changed to <code>2 * sum(x * log(x / E))</code></p></li>
<li><p>Yates' continuity correction was removed as it does not apply to a <em>G</em>-test</p></li>
<li><p>The possibility to simulate p values with <code>simulate.p.value</code> was removed</p></li>
</ul>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list with class <code>"htest"</code> containing the following
components:</p>
<dt>statistic</dt><dd><p>the value the chi-squared test statistic.</p></dd>
<dt>parameter</dt><dd><p>the degrees of freedom of the approximate
chi-squared distribution of the test statistic, <code>NA</code> if the
p-value is computed by Monte Carlo simulation.</p></dd>
<dt>p.value</dt><dd><p>the p-value for the test.</p></dd>
<dt>method</dt><dd><p>a character string indicating the type of test
performed, and whether Monte Carlo simulation or continuity
correction was used.</p></dd>
<dt>data.name</dt><dd><p>a character string giving the name(s) of the data.</p></dd>
<dt>observed</dt><dd><p>the observed counts.</p></dd>
<dt>expected</dt><dd><p>the expected counts under the null hypothesis.</p></dd>
<dt>residuals</dt><dd><p>the Pearson residuals,
<code>(observed - expected) / sqrt(expected)</code>.</p></dd>
<dt>stdres</dt><dd><p>standardized residuals,
<code>(observed - expected) / sqrt(V)</code>, where <code>V</code> is the residual cell variance (Agresti, 2007,
section 2.4.5 for the case where <code>x</code> is a matrix, <code>n * p * (1 - p)</code> otherwise).</p></dd>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>If <code>x</code> is a matrix with one row or column, or if <code>x</code> is a vector and <code>y</code> is not given, then a <em>goodness-of-fit test</em> is performed (<code>x</code> is treated as a one-dimensional contingency table). The entries of <code>x</code> must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in <code>p</code>, or are all equal if <code>p</code> is not given.</p>
<p>If <code>x</code> is a matrix with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of <code>x</code> must be non-negative integers. Otherwise, <code>x</code> and <code>y</code> must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.</p>
<p>The p-value is computed from the asymptotic chi-squared distribution of the test statistic.</p>
<p>In the contingency table case simulation is done by random sampling from the set of all contingency tables with given marginals, and works only if the marginals are strictly positive. Note that this is not the usual sampling situation assumed for a chi-squared test (like the <em>G</em>-test) but rather that for Fisher's exact test.</p>
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p>
<h2 class="hasAnchor" id="g-test-of-goodness-of-fit-likelihood-ratio-test-"><a class="anchor" href="#g-test-of-goodness-of-fit-likelihood-ratio-test-"></a><em>G</em>-test of goodness-of-fit (likelihood ratio test)</h2>
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://www.rdocumentation.org/packages/stats/topics/fisher.test'>fisher.test</a></code>).</p>
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://www.rdocumentation.org/packages/stats/topics/chisq.test'>chisq.test</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p>
<h2 class="hasAnchor" id="g-test-of-independence"><a class="anchor" href="#g-test-of-independence"></a><em>G</em>-test of independence</h2>
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
<p>It is also possible to do a <em>G</em>-test of independence with more than two nominal variables. For example, Jackson et al. (2013) also had data for children under 3, so you could do an analysis of old vs. young, thigh vs. arm, and reaction vs. no reaction, all analyzed together.</p>
<p>Fisher's exact test (<code><a href='https://www.rdocumentation.org/packages/stats/topics/fisher.test'>fisher.test</a></code>) is more accurate than the <em>G</em>-test of independence when the expected numbers are small, so it is recommend to only use the <em>G</em>-test if your total sample size is greater than 1000.</p>
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://www.rdocumentation.org/packages/stats/topics/chisq.test'>chisq.test</a></code>), and they will give approximately the same results.</p>
<h2 class="hasAnchor" id="how-the-test-works"><a class="anchor" href="#how-the-test-works"></a>How the test works</h2>
<p>Unlike the exact test of goodness-of-fit (<code><a href='https://www.rdocumentation.org/packages/stats/topics/fisher.test'>fisher.test</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
<p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
<p><code>G &lt;- 2 * sum(x * log(x / E))</code></p>
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated with:</p>
<p><code>p &lt;- stats::pchisq(G, df, lower.tail = FALSE)</code></p>
<p>where <code>df</code> are the degrees of freedom.</p>
<p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>[1] McDonald, J.H. 2014. <strong>Handbook of Biological Statistics (3rd ed.)</strong>. Sparky House Publishing, Baltimore, Maryland. <a href='http://www.biostathandbook.com/gtestgof.html'>http://www.biostathandbook.com/gtestgof.html</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='https://www.rdocumentation.org/packages/stats/topics/chisq.test'>chisq.test</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># = EXAMPLE 1 =</span>
<span class='co'># Shivrain et al. (2006) crossed clearfield rice (which are resistant</span>
<span class='co'># to the herbicide imazethapyr) with red rice (which are susceptible to</span>
<span class='co'># imazethapyr). They then crossed the hybrid offspring and examined the</span>
<span class='co'># F2 generation, where they found 772 resistant plants, 1611 moderately</span>
<span class='co'># resistant plants, and 737 susceptible plants. If resistance is controlled</span>
<span class='co'># by a single gene with two co-dominant alleles, you would expect a 1:2:1</span>
<span class='co'># ratio.</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>772</span>, <span class='fl'>1611</span>, <span class='fl'>737</span>)<span class='co'>#'</span>
<span class='no'>G</span> <span class='kw'>&lt;-</span> <span class='fu'>g.test</span>(<span class='no'>x</span>, <span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>1</span>) / <span class='fl'>4</span>)
<span class='co'># G$p.value = 0.12574.</span>
<span class='co'># There is no significant difference from a 1:2:1 ratio.</span>
<span class='co'># Meaning: resistance controlled by a single gene with two co-dominant</span>
<span class='co'># alleles, is plausible.</span>
<span class='co'># = EXAMPLE 2 =</span>
<span class='co'># Red crossbills (Loxia curvirostra) have the tip of the upper bill either</span>
<span class='co'># right or left of the lower bill, which helps them extract seeds from pine</span>
<span class='co'># cones. Some have hypothesized that frequency-dependent selection would</span>
<span class='co'># keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992)</span>
<span class='co'># observed 1752 right-billed and 1895 left-billed crossbills.</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1752</span>, <span class='fl'>1895</span>)
<span class='fu'>g.test</span>(<span class='no'>x</span>)
<span class='co'># p = 0.01787343</span>
<span class='co'># There is a significant difference from a 1:1 ratio.</span>
<span class='co'># Meaning: there are significantly more left-billed birds.</span>
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#g-test-of-goodness-of-fit-likelihood-ratio-test-"><em>G</em>-test of goodness-of-fit (likelihood ratio test)</a></li>
<li><a href="#g-test-of-independence"><em>G</em>-test of independence</a></li>
<li><a href="#how-the-test-works">How the test works</a></li>
<li><a href="#references">References</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
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<h1>Get language for AMR</h1>
<div class="hidden name"><code>get_locale.Rd</code></div>
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<div class="ref-description">
<p>Determines the system language to be used for language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_gramstain</a></code> and <code><a href='mo_property.html'>mo_type</a></code>.</p>
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<pre class="usage"><span class='fu'>get_locale</span>()</pre>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</p>
<h2 class="hasAnchor" id="supported-languages"><a class="anchor" href="#supported-languages"></a>Supported languages</h2>
<p>Supported languages are <code>"en"</code> (English), <code>"de"</code> (German), <code>"nl"</code> (Dutch), <code>"es"</code> (Spanish), <code>"it"</code> (Italian), <code>"fr"</code> (French), and <code>"pt"</code> (Portuguese).</p>
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<h1>AMR bar plots with <code>ggplot</code></h1>
<div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div>
<div class="ref-description">
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> functions.</p>
</div>
<pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
<span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"official"</span>, <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"grey15"</span>, <span class='no'>...</span>)
<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Antibiotic"</span>, <span class='st'>"Interpretation"</span>),
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"official"</span>, <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
<span class='no'>...</span>)
<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Interpretation"</span>, <span class='st'>"Antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>scale_rsi_colours</span>()
<span class='fu'>theme_rsi</span>()
<span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"grey15"</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>data</th>
<td><p>a <code>data.frame</code> with column(s) of class <code>"rsi"</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>)</p></td>
</tr>
<tr>
<th>position</th>
<td><p>position adjustment of bars, either <code>"fill"</code> (default when <code>fun</code> is <code><a href='count.html'>count_df</a></code>), <code>"stack"</code> (default when <code>fun</code> is <code><a href='portion.html'>portion_df</a></code>) or <code>"dodge"</code></p></td>
</tr>
<tr>
<th>x</th>
<td><p>variable to show on x axis, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td>
</tr>
<tr>
<th>fill</th>
<td><p>variable to categorise using the plots legend, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td>
</tr>
<tr>
<th>facet</th>
<td><p>variable to split plots by, either <code>"Interpretation"</code> (default) or <code>"Antibiotic"</code> or a grouping variable</p></td>
</tr>
<tr>
<th>breaks</th>
<td><p>numeric vector of positions</p></td>
</tr>
<tr>
<th>limits</th>
<td><p>numeric vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum</p></td>
</tr>
<tr>
<th>translate_ab</th>
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations into, using <code><a href='abname.html'>abname</a></code>. Default behaviour is to translate to official names according to the WHO. Use <code>translate_ab = FALSE</code> to disable translation.</p></td>
</tr>
<tr>
<th>fun</th>
<td><p>function to transform <code>data</code>, either <code><a href='count.html'>count_df</a></code> (default) or <code><a href='portion.html'>portion_df</a></code></p></td>
</tr>
<tr>
<th>nrow</th>
<td><p>(when using <code>facet</code>) number of rows</p></td>
</tr>
<tr>
<th>datalabels</th>
<td><p>show datalabels using <code>labels_rsi_count</code>, will at default only be shown when <code>fun = count_df</code></p></td>
</tr>
<tr>
<th>datalabels.size</th>
<td><p>size of the datalabels</p></td>
</tr>
<tr>
<th>datalabels.colour</th>
<td><p>colour of the datalabels</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to <code>geom_rsi</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='abname.html'>abname</a></code>. This can be set with the option <code>get_antibiotic_names</code> (a logical value), so change it e.g. to <code>FALSE</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options(get_antibiotic_names = FALSE)</a></code>.</p>
<p><strong>The functions</strong><br />
<code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>facet_wrap</a></code>.</p>
<p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p>
<p><code>scale_rsi_colours</code> sets colours to the bars: green for S, yellow for I and red for R, using <code>scale_brewer</code>.</p>
<p><code>theme_rsi</code> is a <code>ggplot <a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></code> with minimal distraction.</p>
<p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>geom_text</a></code></p>
<p><code>ggplot_rsi</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>)
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
<span class='fu'>geom_rsi</span>()
<span class='co'># prettify the plot using some additional functions:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span>[, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"nitr"</span>, <span class='st'>"fosf"</span>, <span class='st'>"trim"</span>, <span class='st'>"cipr"</span>)]
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
<span class='fu'>geom_rsi</span>() +
<span class='fu'>scale_y_percent</span>() +
<span class='fu'>scale_rsi_colours</span>() +
<span class='fu'>labels_rsi_count</span>() +
<span class='fu'>theme_rsi</span>()
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>()
<span class='co'># get only portions and no counts:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>portion_df</span>)
<span class='co'># add other ggplot2 parameters as you like:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
<span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>linetype</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># `age_group` is also a function of this package:</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>)
<span class='co'># genuine analysis: check 2 most prevalent microorganisms</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on top three bacterial ID's</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># determine first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
<span class='co'># get short MO names (like "E. coli")</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># select this short name and some antiseptic drugs</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='co'># group by MO</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='co'># plot the thing, putting MOs on the facet</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='st'>"Only First Isolates, CoNS grouped according to Becker et al. (2014)"</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Microorganisms"</span>)
<span class='co'># }</span></pre>
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<h1>Reference</h1>
</div>
<table class="ref-index">
<colgroup>
<col class="alias" />
<col class="title" />
</colgroup>
<tbody>
<tr>
<th colspan="2">
<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
<p class="section-desc"><p>Functions for cleaning and optimising your data, to be able to add variables later on (like taxonomic properties) or to fix and extend antibiotic interpretations by applying EUCAST rules.</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="as.atc.html">as.atc()</a></code> <code><a href="as.atc.html">guess_atc()</a></code> <code><a href="as.atc.html">is.atc()</a></code> </p>
</td>
<td><p>Transform to ATC code</p></td>
</tr><tr>
<td>
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
</td>
<td><p>Class 'mic'</p></td>
</tr><tr>
<td>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">guess_mo()</a></code> </p>
</td>
<td><p>Transform to microorganism ID</p></td>
</tr><tr>
<td>
<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
</td>
<td><p>Class 'rsi'</p></td>
</tr><tr>
<td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">EUCAST_rules()</a></code> <code><a href="eucast_rules.html">interpretive_reading()</a></code> </p>
</td>
<td><p>EUCAST rules</p></td>
</tr><tr>
<td>
<p><code><a href="read.4D.html">read.4D()</a></code> </p>
</td>
<td><p>Read data from 4D database</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2>
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates,</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
</td>
<td><p>Determine first (weighted) isolates</p></td>
</tr><tr>
<td>
<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
</td>
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
</tr><tr>
<td>
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
</td>
<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_subkingdom()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_TSN()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>
<td>
<p><code><a href="ab_property.html">ab_property()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_official()</a></code> <code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_trivial_nl()</a></code> <code><a href="ab_property.html">ab_certe()</a></code> <code><a href="ab_property.html">ab_umcg()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> </p>
</td>
<td><p>Property of an antibiotic</p></td>
</tr><tr>
<td>
<p><code><a href="atc_property.html">atc_property()</a></code> <code><a href="atc_property.html">atc_groups()</a></code> <code><a href="atc_property.html">atc_ddd()</a></code> </p>
</td>
<td><p>Properties of an ATC code</p></td>
</tr><tr>
<td>
<p><code><a href="abname.html">abname()</a></code> </p>
</td>
<td><p>Name of an antibiotic</p></td>
</tr><tr>
<td>
<p><code><a href="age.html">age()</a></code> </p>
</td>
<td><p>Age in years of individuals</p></td>
</tr><tr>
<td>
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
</td>
<td><p>Split ages into age groups</p></td>
</tr><tr>
<td>
<p><code><a href="p.symbol.html">p.symbol()</a></code> </p>
</td>
<td><p>Symbol of a p value</p></td>
</tr><tr>
<td>
<p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
</td>
<td><p>Join a table with <code>microorganisms</code></p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-analysing-the-data" class="hasAnchor"><a href="#section-analysing-the-data" class="anchor"></a>Analysing the data</h2>
<p class="section-desc"><p>Functions for conducting AMR analysis</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
</td>
<td><p>Count isolates</p></td>
</tr><tr>
<td>
<p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> </p>
</td>
<td><p>Calculate resistance of isolates</p></td>
</tr><tr>
<td>
<p><code><a href="freq.html">frequency_tbl()</a></code> <code><a href="freq.html">freq()</a></code> <code><a href="freq.html">top_freq()</a></code> <code><a href="freq.html">header()</a></code> <code><a href="freq.html">print(<i>&lt;frequency_tbl&gt;</i>)</a></code> </p>
</td>
<td><p>Frequency table</p></td>
</tr><tr>
<td>
<p><code><a href="g.test.html">g.test()</a></code> </p>
</td>
<td><p><em>G</em>-test for Count Data</p></td>
</tr><tr>
<td>
<p><code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code> </p>
</td>
<td><p>AMR bar plots with <code>ggplot</code></p></td>
</tr><tr>
<td>
<p><code><a href="kurtosis.html">kurtosis()</a></code> </p>
</td>
<td><p>Kurtosis of the sample</p></td>
</tr><tr>
<td>
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> </p>
</td>
<td><p>Predict antimicrobial resistance</p></td>
</tr><tr>
<td>
<p><code><a href="rsi.html">rsi()</a></code> </p>
</td>
<td><p>Calculate resistance of isolates</p></td>
</tr><tr>
<td>
<p><code><a href="skewness.html">skewness()</a></code> </p>
</td>
<td><p>Skewness of the sample</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-included-data-sets" class="hasAnchor"><a href="#section-included-data-sets" class="anchor"></a>Included data sets</h2>
<p class="section-desc"><p>References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="antibiotics.html">antibiotics</a></code> </p>
</td>
<td><p>Data set with 423 antibiotics</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with taxonomic data from ITIS</p></td>
</tr><tr>
<td>
<p><code><a href="septic_patients.html">septic_patients</a></code> </p>
</td>
<td><p>Data set with 2000 blood culture isolates of septic patients</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.certe.html">microorganisms.certe</a></code> </p>
</td>
<td><p>Translation table for Certe</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
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<td><p>Data set with old taxonomic data from ITIS</p></td>
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<p><code><a href="microorganisms.umcg.html">microorganisms.umcg</a></code> </p>
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<td><p>Translation table for UMCG</p></td>
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<p><code><a href="supplementary_data.html">microorganismsDT</a></code> <code><a href="supplementary_data.html">microorganisms.prevDT</a></code> <code><a href="supplementary_data.html">microorganisms.unprevDT</a></code> <code><a href="supplementary_data.html">microorganisms.oldDT</a></code> </p>
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<td><p>Supplementary Data</p></td>
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<h2 id="section-other" class="hasAnchor"><a href="#section-other" class="anchor"></a>Other</h2>
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<td><p>Get language for AMR</p></td>
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<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> </p>
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<td><p>Pattern Matching</p></td>
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<p><code><a href="mo_failures.html">mo_failures()</a></code> </p>
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<td><p>Vector of failed coercion attempts</p></td>
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<p><code><a href="mo_renamed.html">mo_renamed()</a></code> </p>
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<td><p>Vector of taxonomic renamed items</p></td>
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<h1>Join a table with <code>microorganisms</code></h1>
<div class="hidden name"><code>join.Rd</code></div>
</div>
<div class="ref-description">
<p>Join the dataset <code><a href='microorganisms.html'>microorganisms</a></code> easily to an existing table or character vector.</p>
</div>
<pre class="usage"><span class='fu'>inner_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<span class='fu'>left_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<span class='fu'>right_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<span class='fu'>full_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='no'>...</span>)
<span class='fu'>semi_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
<span class='fu'>anti_join_microorganisms</span>(<span class='no'>x</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>existing table to join, or character vector</p></td>
</tr>
<tr>
<th>by</th>
<td><p>a variable to join by - if left empty will search for a column with class <code>mo</code> (created with <code><a href='as.mo.html'>as.mo</a></code>) or will be <code>"mo"</code> if that column name exists in <code>x</code>, could otherwise be a column name of <code>x</code> with values that exist in <code>microorganisms$mo</code> (like <code>by = "bacteria_id"</code>), or another column in <code><a href='microorganisms.html'>microorganisms</a></code> (but then it should be named, like <code>by = c("my_genus_species" = "fullname")</code>)</p></td>
</tr>
<tr>
<th>suffix</th>
<td><p>if there are non-joined duplicate variables in <code>x</code> and <code>y</code>, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters to pass on to <code>dplyr::<a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Note:</strong> As opposed to the <code><a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code> functions of <code>dplyr</code>, characters vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code> for more information.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))
<span class='fu'>left_join_microorganisms</span>(<span class='st'>"B_KLBSL_PNE"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>left_join_microorganisms</span>()
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='kw'>from</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/as.Date'>as.Date</a></span>(<span class='st'>"2018-01-01"</span>),
<span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/as.Date'>as.Date</a></span>(<span class='st'>"2018-01-07"</span>),
<span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>1</span>),
<span class='kw'>bacteria</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"S. aureus"</span>, <span class='st'>"MRSA"</span>, <span class='st'>"MSSA"</span>, <span class='st'>"STAAUR"</span>,
<span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>)),
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>colnames</a></span>(<span class='no'>df</span>)
<span class='no'>df_joined</span> <span class='kw'>&lt;-</span> <span class='fu'>left_join_microorganisms</span>(<span class='no'>df</span>, <span class='st'>"bacteria"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>colnames</a></span>(<span class='no'>df_joined</span>)
<span class='co'># }</span></pre>
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<h1>Key antibiotics for first <em>weighted</em> isolates</h1>
<div class="hidden name"><code>key_antibiotics.Rd</code></div>
</div>
<div class="ref-description">
<p>These function can be used to determine first isolates (see <code><a href='first_isolate.html'>first_isolate</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first <em>weighted</em> isolates.</p>
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='st'>"pita"</span>,
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>,
<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='st'>"teic"</span>, <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>,
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='st'>"gent"</span>,
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>, <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>,
<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tbl</th>
<td><p>table with antibiotics coloms, like <code>amox</code> and <code>amcl</code>.</p></td>
</tr>
<tr>
<th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr>
<tr>
<th>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th>
<td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive</p></td>
</tr>
<tr>
<th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
<td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive</p></td>
</tr>
<tr>
<th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
<td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive</p></td>
</tr>
<tr>
<th>warnings</th>
<td><p>give warning about missing antibiotic columns, they will anyway be ignored</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to function</p></td>
</tr>
<tr>
<th>x, y</th>
<td><p>characters to compare</p></td>
</tr>
<tr>
<th>type</th>
<td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see Details</p></td>
</tr>
<tr>
<th>ignore_I</th>
<td><p>logical to determine whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see Details</p></td>
</tr>
<tr>
<th>points_threshold</th>
<td><p>points until the comparison of key antibiotics will lead to inclusion of an isolate when <code>type = "points"</code>, see Details</p></td>
</tr>
<tr>
<th>info</th>
<td><p>print progress</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it wouldn't.</p>
<p>At default, the antibiotics that are used for <strong>Gram positive bacteria</strong> are (colum names): <br />
<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"vanc"</code>, <code>"teic"</code>, <code>"tetr"</code>, <code>"eryt"</code>, <code>"oxac"</code>, <code>"rifa"</code>.</p>
<p>At default, the antibiotics that are used for <strong>Gram negative bacteria</strong> are (colum names): <br />
<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"gent"</code>, <code>"tobr"</code>, <code>"coli"</code>, <code>"cfot"</code>, <code>"cfta"</code>, <code>"mero"</code>.</p>
<p>The function <code>key_antibiotics_equal</code> checks the characters returned by <code>key_antibiotics</code> for equality, and returns a logical vector.</p>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
<p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results: <br /></p>
<p><strong>1. Using</strong> <code>type = "keyantibiotics"</code> <strong>and parameter</strong> <code>ignore_I</code> <br />
Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. <br /></p>
<p><strong>2. Using</strong> <code>type = "points"</code> <strong>and parameter</strong> <code>points_threshold</code> <br />
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, an isolate will be (re)selected as a first weighted isolate.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a dataset available in the AMR package</span>
?<span class='no'>septic_patients</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
<span class='co'># now calculate first isolates</span>
<span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
<span class='co'># and first WEIGHTED isolates</span>
<span class='kw'>first_weighted</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>"keyab"</span>)
)
<span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'># output of the `key_antibiotics` function could be like this:</span>
<span class='no'>strainA</span> <span class='kw'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>
<span class='no'>strainB</span> <span class='kw'>&lt;-</span> <span class='st'>"SSSIRSSSRSSS"</span>
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>)
<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span>
<span class='co'># }</span></pre>
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#key-antibiotics">Key antibiotics</a></li>
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<li><a href="#examples">Examples</a></li>
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<h1>Kurtosis of the sample</h1>
<div class="hidden name"><code>kurtosis.Rd</code></div>
</div>
<div class="ref-description">
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.</p>
</div>
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># S3 method for default</span>
<span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># S3 method for matrix</span>
<span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># S3 method for data.frame</span>
<span class='fu'>kurtosis</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<th>x</th>
<td><p>a vector of values, a <code>matrix</code> or a <code>data frame</code></p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical value indicating whether <code>NA</code> values should be stripped before the computation proceeds.</p></td>
</tr>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='skewness.html'>skewness</a></code></p></div>
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<meta property="og:description" content="Convenient wrapper around grep to match a pattern: a %like% b. It always returns a logical vector and is always case-insensitive. Also, pattern (b) can be as long as x (a) to compare items of each index in both vectors." />
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<h1>Pattern Matching</h1>
<div class="hidden name"><code>like.Rd</code></div>
</div>
<div class="ref-description">
<p>Convenient wrapper around <code><a href='https://www.rdocumentation.org/packages/base/topics/grep'>grep</a></code> to match a pattern: <code>a %like% b</code>. It always returns a <code>logical</code> vector and is always case-insensitive. Also, <code>pattern</code> (<code>b</code>) can be as long as <code>x</code> (<code>a</code>) to compare items of each index in both vectors.</p>
</div>
<pre class="usage"><span class='fu'>like</span>(<span class='no'>x</span>, <span class='no'>pattern</span>)
<span class='no'>x</span> <span class='kw'>%like%</span> <span class='no'>pattern</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a character vector where matches are sought, or an
object which can be coerced by <code>as.character</code> to a character
vector. <a href='https://www.rdocumentation.org/packages/base/topics/LongVectors'>Long vectors</a> are supported.</p></td>
</tr>
<tr>
<th>pattern</th>
<td><p>character string containing a <a href='https://www.rdocumentation.org/packages/base/topics/regex'>regular expression</a>
(or character string for <code>fixed = TRUE</code>) to be matched
in the given character vector. Coerced by
<code><a href='https://www.rdocumentation.org/packages/base/topics/character'>as.character</a></code> to a character string if possible. If a
character vector of length 2 or more is supplied, the first element
is used with a warning. Missing values are allowed except for
<code>regexpr</code> and <code>gregexpr</code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/master/R/like.R'><code>like</code> function from the <code>data.table</code> package</a>, but made it case insensitive at default and let it support multiple patterns.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A <code>logical</code> vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like Ctrl+Shift+L or Cmd+Shift+L (see Tools &gt; Modify Keyboard Shortcuts...).</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='https://www.rdocumentation.org/packages/base/topics/grep'>grep</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># simple test</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='st'>"This is a test"</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='st'>"TEST"</span>
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='co'>#&gt; TRUE</span>
<span class='no'>b</span> <span class='kw'>%like%</span> <span class='no'>a</span>
<span class='co'>#&gt; FALSE</span>
<span class='co'># also supports multiple patterns, length must be equal to x</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span>)
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='co'>#&gt; TRUE TRUE TRUE</span>
<span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)
<span class='co'># }</span></pre>
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<h1>Determine multidrug-resistant organisms (MDRO)</h1>
<div class="hidden name"><code>mdro.Rd</code></div>
</div>
<div class="ref-description">
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.</p>
</div>
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>amik</span> <span class='kw'>=</span> <span class='st'>"amik"</span>, <span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='st'>"ampi"</span>,
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='st'>"azit"</span>, <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='st'>"aztr"</span>, <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='st'>"cefa"</span>, <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='st'>"cfra"</span>,
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='st'>"cfep"</span>, <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>, <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"cfox"</span>, <span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>,
<span class='kw'>cftr</span> <span class='kw'>=</span> <span class='st'>"cftr"</span>, <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='st'>"chlo"</span>, <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>,
<span class='kw'>clar</span> <span class='kw'>=</span> <span class='st'>"clar"</span>, <span class='kw'>clin</span> <span class='kw'>=</span> <span class='st'>"clin"</span>, <span class='kw'>clox</span> <span class='kw'>=</span> <span class='st'>"clox"</span>, <span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"coli"</span>,
<span class='kw'>czol</span> <span class='kw'>=</span> <span class='st'>"czol"</span>, <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='st'>"dapt"</span>, <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='st'>"doxy"</span>, <span class='kw'>erta</span> <span class='kw'>=</span> <span class='st'>"erta"</span>,
<span class='kw'>eryt</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>, <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='st'>"fosf"</span>, <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='st'>"fusi"</span>, <span class='kw'>gent</span> <span class='kw'>=</span> <span class='st'>"gent"</span>,
<span class='kw'>imip</span> <span class='kw'>=</span> <span class='st'>"imip"</span>, <span class='kw'>kana</span> <span class='kw'>=</span> <span class='st'>"kana"</span>, <span class='kw'>levo</span> <span class='kw'>=</span> <span class='st'>"levo"</span>, <span class='kw'>linc</span> <span class='kw'>=</span> <span class='st'>"linc"</span>,
<span class='kw'>line</span> <span class='kw'>=</span> <span class='st'>"line"</span>, <span class='kw'>mero</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>metr</span> <span class='kw'>=</span> <span class='st'>"metr"</span>, <span class='kw'>mino</span> <span class='kw'>=</span> <span class='st'>"mino"</span>,
<span class='kw'>moxi</span> <span class='kw'>=</span> <span class='st'>"moxi"</span>, <span class='kw'>nali</span> <span class='kw'>=</span> <span class='st'>"nali"</span>, <span class='kw'>neom</span> <span class='kw'>=</span> <span class='st'>"neom"</span>, <span class='kw'>neti</span> <span class='kw'>=</span> <span class='st'>"neti"</span>,
<span class='kw'>nitr</span> <span class='kw'>=</span> <span class='st'>"nitr"</span>, <span class='kw'>novo</span> <span class='kw'>=</span> <span class='st'>"novo"</span>, <span class='kw'>norf</span> <span class='kw'>=</span> <span class='st'>"norf"</span>, <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='st'>"oflo"</span>,
<span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"peni"</span>, <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='st'>"pipe"</span>, <span class='kw'>pita</span> <span class='kw'>=</span> <span class='st'>"pita"</span>, <span class='kw'>poly</span> <span class='kw'>=</span> <span class='st'>"poly"</span>,
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='st'>"qida"</span>, <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='st'>"roxi"</span>, <span class='kw'>siso</span> <span class='kw'>=</span> <span class='st'>"siso"</span>,
<span class='kw'>teic</span> <span class='kw'>=</span> <span class='st'>"teic"</span>, <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>tica</span> <span class='kw'>=</span> <span class='st'>"tica"</span>, <span class='kw'>tige</span> <span class='kw'>=</span> <span class='st'>"tige"</span>,
<span class='kw'>tobr</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>, <span class='kw'>trim</span> <span class='kw'>=</span> <span class='st'>"trim"</span>, <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>)
<span class='fu'>brmo</span>(<span class='no'>...</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
<span class='fu'>mrgn</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"de"</span>, <span class='no'>...</span>)
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tbl</th>
<td><p>table with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td>
</tr>
<tr>
<th>country</th>
<td><p>country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the <a href='https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements'>list of ISO 3166-1 alpha-2 country codes</a>. Case-insensitive. Currently supported are <code>de</code> (Germany) and <code>nl</code> (the Netherlands).</p></td>
</tr>
<tr>
<th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr>
<tr>
<th>info</th>
<td><p>print progress</p></td>
</tr>
<tr>
<th>amcl</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>amik</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>amox</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>ampi</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>azit</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>aztr</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cefa</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cfra</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cfep</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cfot</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cfox</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cfta</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cftr</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cfur</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>chlo</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>cipr</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>clar</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>clin</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>clox</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>coli</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>czol</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>dapt</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>doxy</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>erta</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>eryt</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>fosf</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>fusi</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>gent</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>imip</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>kana</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>levo</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>linc</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>line</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>mero</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>metr</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>mino</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>moxi</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>nali</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>neom</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>neti</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>nitr</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>novo</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>norf</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>oflo</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>peni</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>pipe</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>pita</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>poly</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>qida</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>rifa</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>roxi</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>siso</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>teic</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>tetr</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>tica</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>tige</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>tobr</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>trim</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>trsu</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>vanc</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>...</th>
<td><p>parameters that are passed on to methods</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered factor with levels <code>Negative &lt; Positive, unconfirmed &lt; Positive</code>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>When <code>country</code> will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a>).</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
<p>To define antibiotics column names, input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>),
<strong>amox</strong>: amoxicillin (<em>J01CA04</em>),
<strong>ampi</strong>: ampicillin (<em>J01CA01</em>),
<strong>azit</strong>: azithromycin (<em>J01FA10</em>),
<strong>azlo</strong>: azlocillin (<em>J01CA09</em>),
<strong>aztr</strong>: aztreonam (<em>J01DF01</em>),
<strong>cefa</strong>: cefaloridine (<em>J01DB02</em>),
<strong>cfep</strong>: cefepime (<em>J01DE01</em>),
<strong>cfot</strong>: cefotaxime (<em>J01DD01</em>),
<strong>cfox</strong>: cefoxitin (<em>J01DC01</em>),
<strong>cfra</strong>: cefradine (<em>J01DB09</em>),
<strong>cfta</strong>: ceftazidime (<em>J01DD02</em>),
<strong>cftr</strong>: ceftriaxone (<em>J01DD04</em>),
<strong>cfur</strong>: cefuroxime (<em>J01DC02</em>),
<strong>chlo</strong>: chloramphenicol (<em>J01BA01</em>),
<strong>cipr</strong>: ciprofloxacin (<em>J01MA02</em>),
<strong>clar</strong>: clarithromycin (<em>J01FA09</em>),
<strong>clin</strong>: clindamycin (<em>J01FF01</em>),
<strong>clox</strong>: flucloxacillin (<em>J01CF05</em>),
<strong>coli</strong>: colistin (<em>J01XB01</em>),
<strong>czol</strong>: cefazolin (<em>J01DB04</em>),
<strong>dapt</strong>: daptomycin (<em>J01XX09</em>),
<strong>doxy</strong>: doxycycline (<em>J01AA02</em>),
<strong>erta</strong>: ertapenem (<em>J01DH03</em>),
<strong>eryt</strong>: erythromycin (<em>J01FA01</em>),
<strong>fosf</strong>: fosfomycin (<em>J01XX01</em>),
<strong>fusi</strong>: fusidic acid (<em>J01XC01</em>),
<strong>gent</strong>: gentamicin (<em>J01GB03</em>),
<strong>imip</strong>: imipenem (<em>J01DH51</em>),
<strong>kana</strong>: kanamycin (<em>J01GB04</em>),
<strong>levo</strong>: levofloxacin (<em>J01MA12</em>),
<strong>linc</strong>: lincomycin (<em>J01FF02</em>),
<strong>line</strong>: linezolid (<em>J01XX08</em>),
<strong>mero</strong>: meropenem (<em>J01DH02</em>),
<strong>mezl</strong>: mezlocillin (<em>J01CA10</em>),
<strong>mino</strong>: minocycline (<em>J01AA08</em>),
<strong>moxi</strong>: moxifloxacin (<em>J01MA14</em>),
<strong>nali</strong>: nalidixic acid (<em>J01MB02</em>),
<strong>neom</strong>: neomycin (<em>J01GB05</em>),
<strong>neti</strong>: netilmicin (<em>J01GB07</em>),
<strong>nitr</strong>: nitrofurantoin (<em>J01XE01</em>),
<strong>norf</strong>: norfloxacin (<em>J01MA06</em>),
<strong>novo</strong>: novobiocin (an ATCvet code: <em>QJ01XX95</em>),
<strong>oflo</strong>: ofloxacin (<em>J01MA01</em>),
<strong>peni</strong>: penicillin (<em>J01RA01</em>),
<strong>pipe</strong>: piperacillin (<em>J01CA12</em>),
<strong>pita</strong>: piperacillin+tazobactam (<em>J01CR05</em>),
<strong>poly</strong>: polymyxin B (<em>J01XB02</em>),
<strong>pris</strong>: pristinamycin (<em>J01FG01</em>),
<strong>qida</strong>: quinupristin/dalfopristin (<em>J01FG02</em>),
<strong>rifa</strong>: rifampicin (<em>J04AB02</em>),
<strong>roxi</strong>: roxithromycin (<em>J01FA06</em>),
<strong>siso</strong>: sisomicin (<em>J01GB08</em>),
<strong>teic</strong>: teicoplanin (<em>J01XA02</em>),
<strong>tetr</strong>: tetracycline (<em>J01AA07</em>),
<strong>tica</strong>: ticarcillin (<em>J01CA13</em>),
<strong>tige</strong>: tigecycline (<em>J01AA12</em>),
<strong>tobr</strong>: tobramycin (<em>J01GB01</em>),
<strong>trim</strong>: trimethoprim (<em>J01EA01</em>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>),
<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>))
<span class='co'># }</span></pre>
</div>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#examples">Examples</a></li>
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<h1>Translation table for Certe</h1>
<div class="hidden name"><code>microorganisms.certe.Rd</code></div>
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<div class="ref-description">
<p>A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='as.mo.html'>guess_mo</a></code>.</p>
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<pre class="usage"><span class='no'>microorganisms.certe</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,665 observations and 2 variables:</p><dl class='dl-horizontal'>
<dt><code>certe</code></dt><dd><p>Code of microorganism according to Certe MMB</p></dd>
<dt><code>mo</code></dt><dd><p>Code of microorganism in <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
</dl>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<h1>Data set with taxonomic data from ITIS</h1>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
<pre class="usage"><span class='no'>microorganisms</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 18,833 observations and 15 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism</p></dd>
<dt><code>tsn</code></dt><dd><p>Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Echerichia coli"</code></p></dd>
<dt><code>family</code></dt><dd><p>Taxonomic family of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>order</code></dt><dd><p>Taxonomic order of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>class</code></dt><dd><p>Taxonomic class of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>phylum</code></dt><dd><p>Taxonomic phylum of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subkingdom</code></dt><dd><p>Taxonomic subkingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>kingdom</code></dt><dd><p>Taxonomic kingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>gramstain</code></dt><dd><p>Gram of microorganism, like <code>"Gram negative"</code></p></dd>
<dt><code>prevalence</code></dt><dd><p>An integer based on estimated prevalence of the microorganism in humans. Used internally by <code><a href='as.mo.html'>as.mo</a></code>, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in ITIS, see Source</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>[3] Integrated Taxonomic Information System (ITIS) on-line database, <a href='https://www.itis.gov'>https://www.itis.gov</a>.</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<p><img src='figures/itis_logo.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.umcg.html'>microorganisms.umcg</a></code></p></div>
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<h1>Data set with old taxonomic data from ITIS</h1>
<div class="hidden name"><code>microorganisms.old.Rd</code></div>
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<p>A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by <code><a href='as.mo.html'>as.mo</a></code>.</p>
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<pre class="usage"><span class='no'>microorganisms.old</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,383 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>tsn</code></dt><dd><p>Old Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>name</code></dt><dd><p>Old taxonomic name of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>tsn_new</code></dt><dd><p>New Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in ITIS, see Source</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>[3] Integrated Taxonomic Information System (ITIS) on-line database, <a href='https://www.itis.gov'>https://www.itis.gov</a>.</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<p><img src='figures/itis_logo.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<meta property="og:description" content="A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from microorganisms$mo (using left_join_microorganisms). GLIMS codes can also be translated to valid MOs with guess_mo." />
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<h1>Translation table for UMCG</h1>
<div class="hidden name"><code>microorganisms.umcg.Rd</code></div>
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<div class="ref-description">
<p>A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='as.mo.html'>guess_mo</a></code>.</p>
</div>
<pre class="usage"><span class='no'>microorganisms.umcg</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 1,095 observations and 2 variables:</p><dl class='dl-horizontal'>
<dt><code>umcg</code></dt><dd><p>Code of microorganism according to UMCG MMB</p></dd>
<dt><code>certe</code></dt><dd><p>Code of microorganism according to Certe MMB</p></dd>
</dl>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='microorganisms.certe.html'>microorganisms.certe</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<h1>Vector of failed coercion attempts</h1>
<div class="hidden name"><code>mo_failures.Rd</code></div>
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<p>Returns a vector of all failed attempts to coerce values to a valid MO code with <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>mo_failures</span>()</pre>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<h1>Property of a microorganism</h1>
<div class="hidden name"><code>mo_property.Rd</code></div>
</div>
<div class="ref-description">
<p>Use these functions to return a specific property of a microorganism from the <code><a href='microorganisms.html'>microorganisms</a></code> data set. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_shortname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_subspecies</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_species</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_genus</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_family</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_order</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_class</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_phylum</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_subkingdom</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_kingdom</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_type</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_TSN</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_ref</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_authors</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_year</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"fullname"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo</a></code></p></td>
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='get_locale.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to <code><a href='as.mo.html'>as.mo</a></code></p></td>
</tr>
<tr>
<th>property</th>
<td><p>one of the column names of one of the <code><a href='microorganisms.html'>microorganisms</a></code> data set or <code>"shortname"</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<ul>
<li><p>An <code>integer</code> in case of <code>mo_TSN</code> and <code>mo_year</code></p></li>
<li><p>A <code>list</code> in case of <code>mo_taxonomy</code></p></li>
<li><p>A <code>character</code> in all other cases</p></li>
</ul>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All functions will return the most recently known taxonomic property according to ITIS, except for <code>mo_ref</code>, <code>mo_authors</code> and <code>mo_year</code>. This leads to the following results:</p><ul>
<li><p><code>mo_fullname("Chlamydia psittaci")</code> will return <code>"Chlamydophila psittaci"</code> (with a warning about the renaming)</p></li>
<li><p><code>mo_ref("Chlamydia psittaci")</code> will return <code>"Page, 1968"</code> (with a warning about the renaming)</p></li>
<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
</ul>
<h2 class="hasAnchor" id="supported-languages"><a class="anchor" href="#supported-languages"></a>Supported languages</h2>
<p>Supported languages are <code>"en"</code> (English), <code>"de"</code> (German), <code>"nl"</code> (Dutch), <code>"es"</code> (Spanish), <code>"it"</code> (Italian), <code>"fr"</code> (French), and <code>"pt"</code> (Portuguese).</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<p><img src='figures/itis_logo.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
<p>[2] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
<p>[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. <a href='http://www.itis.gov'>http://www.itis.gov</a></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='microorganisms.html'>microorganisms</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># All properties of Escherichia coli</span>
<span class='co'>## taxonomic properties</span>
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
<span class='fu'>mo_subkingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Negibacteria"</span>
<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span>
<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span>
<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriales"</span>
<span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriaceae"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>
<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># NA</span>
<span class='fu'>mo_TSN</span>(<span class='st'>"E. coli"</span>) <span class='co'># 285 (Taxonomic Serial Number)</span>
<span class='co'>## colloquial properties</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
<span class='co'>## other properties</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram negative"</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom)</span>
<span class='co'>## scientific reference</span>
<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani and Chalmers, 1919"</span>
<span class='fu'>mo_authors</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani and Chalmers"</span>
<span class='fu'>mo_year</span>(<span class='st'>"E. coli"</span>) <span class='co'># 1919</span>
<span class='co'># Abbreviations known in the field</span>
<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>) <span class='co'># "aureus"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"MRSA"</span>) <span class='co'># "S. aureus"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Gram positive"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"VISA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"VISA"</span>) <span class='co'># "aureus"</span>
<span class='co'># Known subspecies</span>
<span class='fu'>mo_genus</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter"</span>
<span class='fu'>mo_species</span>(<span class='st'>"doylei"</span>) <span class='co'># "jejuni"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter jejuni doylei"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "K. pneumoniae"</span>
<span class='co'># Becker classification, see ?as.mo</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "Staphylococcus epidermidis"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Coagulase Negative Staphylococcus (CoNS)"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "S. epidermidis"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "CoNS"</span>
<span class='co'># Lancefield classification, see ?as.mo</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "Streptococcus pyogenes"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Streptococcus group A"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "S. pyogenes"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "GAS" ('Group A streptococci')</span>
<span class='co'># Language support for German, Dutch, Spanish, Portuguese, Italian and French</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>) <span class='co'># "Gramnegativ"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='co'># "Gram-negatief"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>) <span class='co'># "Gram negativo"</span>
<span class='co'># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on a German system</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bakterien" on a German system</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on an English system</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>) <span class='co'># "Streptococcus Gruppe A"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
<span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='co'># "Streptococcus groep A"</span>
<span class='co'># Get a list with the complete taxonomy (subkingdom to subspecies)</span>
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
<span class='co'># }</span></pre>
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<h1>Vector of taxonomic renamed items</h1>
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<p>Returns a vector of all renamed items of the last coercion to valid MO codes with <code><a href='as.mo.html'>as.mo</a></code>.</p>
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<pre class="usage"><span class='fu'>mo_renamed</span>()</pre>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<p>Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above <code>p = 1</code> will return <code>NA</code>.</p>
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<pre class="usage"><span class='fu'>p.symbol</span>(<span class='no'>p</span>, <span class='kw'>emptychar</span> <span class='kw'>=</span> <span class='st'>" "</span>)</pre>
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<th>p</th>
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portion_R and portion_IR can be used to calculate resistance, portion_S and portion_SI can be used to calculate susceptibility." />
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<h1>Calculate resistance of isolates</h1>
<div class="hidden name"><code>portion.Rd</code></div>
</div>
<div class="ref-description">
<p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>portion_R</code> and <code>portion_IR</code> can be used to calculate resistance, <code>portion_S</code> and <code>portion_SI</code> can be used to calculate susceptibility.<br /></p>
</div>
<pre class="usage"><span class='fu'>portion_R</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_IR</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_I</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_SI</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_S</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"get_antibiotic_names"</span>,
<span class='st'>"official"</span>), <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>...</th>
<td><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href='as.rsi.html'>as.rsi</a></code> if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.</p></td>
</tr>
<tr>
<th>minimum</th>
<td><p>the minimal amount of available isolates. Any number lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
</tr>
<tr>
<th>as_percent</th>
<td><p>a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of <code>0.123456</code> will then be returned as <code>"12.3%"</code>.</p></td>
</tr>
<tr>
<th>also_single_tested</th>
<td><p>a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of <code>portion_S</code> and R in case of <code>portion_R</code>). <strong>This would lead to selection bias in almost all cases.</strong></p></td>
</tr>
<tr>
<th>data</th>
<td><p>a <code>data.frame</code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='abname.html'>abname</a></code>. This can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("get_antibiotic_names")</code>.</p></td>
</tr>
<tr>
<th>combine_IR</th>
<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
<p>Wickham H. <strong>Tidy Data.</strong> The Journal of Statistical Software, vol. 59, 2014. <a href='http://vita.had.co.nz/papers/tidy-data.html'>http://vita.had.co.nz/papers/tidy-data.html</a></p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Double or, when <code>as_percent = TRUE</code>, a character.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. <em>Low counts can infuence the outcome - these <code>portion</code> functions may camouflage this, since they only return the portion albeit being dependent on the <code>minimum</code> parameter.</em></p>
<p><code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
<p>The old <code><a href='rsi.html'>rsi</a></code> function is still available for backwards compatibility but is deprecated.
<br /><br />
To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula:
<div style="text-align: center"><img src='figures/mono_therapy.png' alt='' /></div>
To calculate the probability (<em>p</em>) of susceptibility of more antibiotics (i.e. combination therapy), we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). <br />
<br />
For two antibiotics:
<div style="text-align: center"><img src='figures/combi_therapy_2.png' alt='' /></div>
<br />
For three antibiotics:
<div style="text-align: center"><img src='figures/combi_therapy_3.png' alt='' /></div>
<br />
And so on.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='count.html'>count</a>_*</code> to count resistant and susceptible isolates.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a data set available in the AMR package. It is true, genuine data.</span>
?<span class='no'>septic_patients</span>
<span class='co'># Calculate resistance</span>
<span class='fu'>portion_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>portion_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Or susceptibility</span>
<span class='fu'>portion_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>portion_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Do the above with pipes:</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_R</span>(<span class='no'>amox</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_IR</span>(<span class='no'>amox</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>) <span class='co'># S = 67.1%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>) <span class='co'># n = 1576</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>) <span class='co'># S = 74.0%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>) <span class='co'># n = 1855</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># S = 92.0%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># n = 1517</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>),
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>),
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>, <span class='no'>gent</span>))
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
<span class='no'>my_table</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</span>), <span class='co'># amoxicillin with metronidazole</span>
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amox</span>, <span class='no'>metr</span>))
<span class='co'># }</span></pre>
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<meta property="og:description" content="This function is only useful for the MMB department of the UMCG. Use this function to import data by just defining the file parameter. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with as.mo and transform all antimicrobial columns with as.rsi." />
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<h1>Read data from 4D database</h1>
<div class="hidden name"><code>read.4D.Rd</code></div>
</div>
<div class="ref-description">
<p>This function is only useful for the MMB department of the UMCG. Use this function to <strong>import data by just defining the <code>file</code> parameter</strong>. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with <code><a href='as.mo.html'>as.mo</a></code> and transform all antimicrobial columns with <code><a href='as.rsi.html'>as.rsi</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>read.4D</span>(<span class='no'>file</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='st'>"\"'"</span>, <span class='kw'>dec</span> <span class='kw'>=</span> <span class='st'>","</span>, <span class='kw'>na.strings</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"NA"</span>, <span class='st'>""</span>,
<span class='st'>"."</span>), <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>strip.white</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>blank.lines.skip</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>fileEncoding</span> <span class='kw'>=</span> <span class='st'>"UTF-8"</span>, <span class='kw'>encoding</span> <span class='kw'>=</span> <span class='st'>"UTF-8"</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>file</th>
<td><p>the name of the file which the data are to be read from.
Each row of the table appears as one line of the file. If it does
not contain an <em>absolute</em> path, the file name is
<em>relative</em> to the current working directory,
<code><a href='https://www.rdocumentation.org/packages/base/topics/getwd'>getwd</a>()</code>. Tilde-expansion is performed where supported.
This can be a compressed file (see <code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>file</a></code>).</p>
<p>Alternatively, <code>file</code> can be a readable text-mode
<a href='https://www.rdocumentation.org/packages/base/topics/connections'>connection</a> (which will be opened for reading if
necessary, and if so <code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>close</a></code>d (and hence destroyed) at
the end of the function call). (If <code><a href='https://www.rdocumentation.org/packages/base/topics/showConnections'>stdin</a>()</code> is used,
the prompts for lines may be somewhat confusing. Terminate input
with a blank line or an EOF signal, <code>Ctrl-D</code> on Unix and
<code>Ctrl-Z</code> on Windows. Any pushback on <code><a href='https://www.rdocumentation.org/packages/base/topics/showConnections'>stdin()</a></code> will be
cleared before return.)</p>
<p><code>file</code> can also be a complete URL. (For the supported URL
schemes, see the &#8216;URLs&#8217; section of the help for
<code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>url</a></code>.)</p></td>
</tr>
<tr>
<th>info</th>
<td><p>a logical to indicate whether info about the import should be printed, defaults to <code>TRUE</code> in interactive sessions</p></td>
</tr>
<tr>
<th>header</th>
<td><p>a logical value indicating whether the file contains the
names of the variables as its first line. If missing, the value is
determined from the file format: <code>header</code> is set to <code>TRUE</code>
if and only if the first row contains one fewer field than the
number of columns.</p></td>
</tr>
<tr>
<th>row.names</th>
<td><p>a vector of row names. This can be a vector giving
the actual row names, or a single number giving the column of the
table which contains the row names, or character string giving the
name of the table column containing the row names.</p>
<p>If there is a header and the first row contains one fewer field than
the number of columns, the first column in the input is used for the
row names. Otherwise if <code>row.names</code> is missing, the rows are
numbered.</p>
<p>Using <code>row.names = NULL</code> forces row numbering. Missing or
<code>NULL</code> <code>row.names</code> generate row names that are considered
to be &#8216;automatic&#8217; (and not preserved by <code><a href='https://www.rdocumentation.org/packages/base/topics/matrix'>as.matrix</a></code>).</p></td>
</tr>
<tr>
<th>sep</th>
<td><p>the field separator character. Values on each line of the
file are separated by this character. If <code>sep = ""</code> (the
default for <code>read.table</code>) the separator is &#8216;white space&#8217;,
that is one or more spaces, tabs, newlines or carriage returns.</p></td>
</tr>
<tr>
<th>quote</th>
<td><p>the set of quoting characters. To disable quoting
altogether, use <code>quote = ""</code>. See <code><a href='https://www.rdocumentation.org/packages/base/topics/scan'>scan</a></code> for the
behaviour on quotes embedded in quotes. Quoting is only considered
for columns read as character, which is all of them unless
<code>colClasses</code> is specified.</p></td>
</tr>
<tr>
<th>dec</th>
<td><p>the character used in the file for decimal points.</p></td>
</tr>
<tr>
<th>na.strings</th>
<td><p>a character vector of strings which are to be
interpreted as <code><a href='https://www.rdocumentation.org/packages/base/topics/NA'>NA</a></code> values. Blank fields are also
considered to be missing values in logical, integer, numeric and
complex fields. Note that the test happens <em>after</em>
white space is stripped from the input, so <code>na.strings</code>
values may need their own white space stripped in advance.</p></td>
</tr>
<tr>
<th>skip</th>
<td><p>integer: the number of lines of the data file to skip before
beginning to read data.</p></td>
</tr>
<tr>
<th>check.names</th>
<td><p>logical. If <code>TRUE</code> then the names of the
variables in the data frame are checked to ensure that they are
syntactically valid variable names. If necessary they are adjusted
(by <code><a href='https://www.rdocumentation.org/packages/base/topics/make.names'>make.names</a></code>) so that they are, and also to ensure
that there are no duplicates.</p></td>
</tr>
<tr>
<th>strip.white</th>
<td><p>logical. Used only when <code>sep</code> has
been specified, and allows the stripping of leading and trailing
white space from unquoted <code>character</code> fields (<code>numeric</code> fields
are always stripped). See <code><a href='https://www.rdocumentation.org/packages/base/topics/scan'>scan</a></code> for further details
(including the exact meaning of &#8216;white space&#8217;),
remembering that the columns may include the row names.</p></td>
</tr>
<tr>
<th>fill</th>
<td><p>logical. If <code>TRUE</code> then in case the rows have unequal
length, blank fields are implicitly added. See &#8216;Details&#8217;.</p></td>
</tr>
<tr>
<th>blank.lines.skip</th>
<td><p>logical: if <code>TRUE</code> blank lines in the
input are ignored.</p></td>
</tr>
<tr>
<th>stringsAsFactors</th>
<td><p>logical: should character vectors be converted
to factors? Note that this is overridden by <code>as.is</code> and
<code>colClasses</code>, both of which allow finer control.</p></td>
</tr>
<tr>
<th>fileEncoding</th>
<td><p>character string: if non-empty declares the
encoding used on a file (not a connection) so the character data can
be re-encoded. See the &#8216;Encoding&#8217; section of the help for
<code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>file</a></code>, the &#8216;R Data Import/Export Manual&#8217; and
&#8216;Note&#8217;.</p></td>
</tr>
<tr>
<th>encoding</th>
<td><p>encoding to be assumed for input strings. It is
used to mark character strings as known to be in
Latin-1 or UTF-8 (see <code><a href='https://www.rdocumentation.org/packages/base/topics/Encoding'>Encoding</a></code>): it is not used to
re-encode the input, but allows <span style="R">R</span> to handle encoded strings in
their native encoding (if one of those two). See &#8216;Value&#8217;
and &#8216;Note&#8217;.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.</p>
</div>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
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