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(v1.7.1.9051) updated taxonomy, updated git branch name

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dr. M.S. (Matthijs) Berends
2021-10-06 13:23:57 +02:00
parent 8f5e5a3fc2
commit 37e6e35ec4
139 changed files with 2694 additions and 1862 deletions
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<h1>Deprecated Functions</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<div class="hidden name"><code>AMR-deprecated.Rd</code></div>
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<h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/amr.R'><code>R/amr.R</code></a></small>
<div class="hidden name"><code>AMR.Rd</code></div>
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<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/whocc.R'><code>R/whocc.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/whocc.R'><code>R/whocc.R</code></a></small>
<div class="hidden name"><code>WHOCC.Rd</code></div>
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<h1>Data Set with 500 Isolates - WHONET Example</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>WHONET.Rd</code></div>
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<h1>Retrieve Antimicrobial Drug Names and Doses from Clinical Text</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
<div class="hidden name"><code>ab_from_text.Rd</code></div>
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<h1>Get Properties of an Antibiotic</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<div class="hidden name"><code>ab_property.Rd</code></div>
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<h1>Age in Years of Individuals</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age.Rd</code></div>
</div>

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<h1>Split Ages into Age Groups</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/age.R'><code>R/age.R</code></a></small>
<div class="hidden name"><code>age_groups.Rd</code></div>
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<h1>Antibiotic Selectors</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab_class_selectors.R'><code>R/ab_class_selectors.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/ab_class_selectors.R'><code>R/ab_class_selectors.R</code></a></small>
<div class="hidden name"><code>antibiotic_class_selectors.Rd</code></div>
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<div class="page-header">
<h1>Data Sets with 558 Antimicrobial Drugs</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>antibiotics.Rd</code></div>
</div>
@ -426,13 +426,13 @@
<p>These data sets are available as 'flat files' for use even without <span style="R">R</span> - you can find the files here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt'>https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt'>https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt</a></p></li>
</ul>
<p>Files in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antibiotics.rda'>https://github.com/msberends/AMR/raw/master/data/antibiotics.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/antivirals.rda'>https://github.com/msberends/AMR/raw/master/data/antivirals.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/main/data/antibiotics.rda'>https://github.com/msberends/AMR/raw/main/data/antibiotics.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/main/data/antivirals.rda'>https://github.com/msberends/AMR/raw/main/data/antivirals.rda</a></p></li>
</ul>

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<h1>Transform Input to an Antibiotic ID</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/ab.R'><code>R/ab.R</code></a></small>
<div class="hidden name"><code>as.ab.Rd</code></div>
</div>

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<h1>Transform Input to Disk Diffusion Diameters</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/disk.R'><code>R/disk.R</code></a></small>
<div class="hidden name"><code>as.disk.Rd</code></div>
</div>

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<div class="page-header">
<h1>Transform Input to Minimum Inhibitory Concentrations (MIC)</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mic.R'><code>R/mic.R</code></a></small>
<div class="hidden name"><code>as.mic.Rd</code></div>
</div>

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<div class="page-header">
<h1>Transform Input to a Microorganism Code</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mo.R'><code>R/mo.R</code></a></small>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
@ -378,7 +378,7 @@
<h3 class='hasAnchor' id='machine-readable-interpretation-guidelines'><a class='anchor' aria-hidden='true' href='#machine-readable-interpretation-guidelines'></a>Machine-Readable Interpretation Guidelines</h3>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 22,000 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 22,000 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<h3 class='hasAnchor' id='other'><a class='anchor' aria-hidden='true' href='#other'></a>Other</h3>

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docs/reference/atc_online.html
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<div class="page-header">
<h1>Get ATC Properties from WHOCC Website</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<div class="hidden name"><code>atc_online.Rd</code></div>
</div>

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<div class="page-header">
<h1>Check Availability of Columns</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/availability.R'><code>R/availability.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/availability.R'><code>R/availability.R</code></a></small>
<div class="hidden name"><code>availability.Rd</code></div>
</div>

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<h1>Determine Bug-Drug Combinations</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/bug_drug_combinations.R'><code>R/bug_drug_combinations.R</code></a></small>
<div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
</div>

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<script src="../extra.js"></script>
<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
<meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
<meta property="og:description" content="This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN)." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<meta name="twitter:card" content="summary_large_image" />
<meta name="twitter:creator" content="@msberends" />
@ -93,7 +93,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
@ -243,7 +243,7 @@
</div>
<div class="ref-description">
<p>This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.</p>
<p>This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).</p>
</div>
@ -253,7 +253,7 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p>Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="included-taxa"><a class="anchor" href="#included-taxa"></a>Included Taxa</h2>
@ -269,7 +269,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href='https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
@ -321,7 +321,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
</div>
<div class="pkgdown">

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<h1>Version info of included Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
</div>

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@ -239,7 +239,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<div class="col-md-9 contents">
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<h1>Count Available Isolates</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/count.R'><code>R/count.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/count.R'><code>R/count.R</code></a></small>
<div class="hidden name"><code>count.Rd</code></div>
</div>

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<div class="page-header">
<h1>Define Custom EUCAST Rules</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
<div class="hidden name"><code>custom_eucast_rules.Rd</code></div>
</div>

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<h1>Data Set with Treatment Dosages as Defined by EUCAST</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>dosage.Rd</code></div>
</div>

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@ -94,7 +94,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
@ -341,7 +341,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br /></p>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>March 2021</a>.</p><h3 class='hasAnchor' id='custom-rules'><a class='anchor' aria-hidden='true' href='#custom-rules'></a>Custom Rules</h3>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>5 October 2021</a>.</p><h3 class='hasAnchor' id='custom-rules'><a class='anchor' aria-hidden='true' href='#custom-rules'></a>Custom Rules</h3>
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,

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<h1>Data Set with 2,000 Example Isolates</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>example_isolates.Rd</code></div>
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<h1>Data Set with Unclean Data</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
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<h1>Determine First Isolates</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
<div class="hidden name"><code>first_isolate.Rd</code></div>
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<h1><em>G</em>-test for Count Data</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/g.test.R'><code>R/g.test.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/g.test.R'><code>R/g.test.R</code></a></small>
<div class="hidden name"><code>g.test.Rd</code></div>
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<h1>Determine (New) Episodes for Patients</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/episode.R'><code>R/episode.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/episode.R'><code>R/episode.R</code></a></small>
<div class="hidden name"><code>get_episode.Rd</code></div>
</div>

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<h1>PCA Biplot with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
<div class="hidden name"><code>ggplot_pca.Rd</code></div>
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<h1>AMR Plots with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
<div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div>

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<h1>Guess Antibiotic Column</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
<div class="hidden name"><code>guess_ab_col.Rd</code></div>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
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<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data Set with 70,026 Microorganisms</p></td>
<td><p>Data Set with 70,760 Microorganisms</p></td>
</tr><tr>
<td>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
@ -258,7 +258,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
<p>This data set is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020).</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
@ -292,7 +292,7 @@
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
</div>
<div class="pkgdown">

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<h1>Italicise Taxonomic Families, Genera, Species, Subspecies</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/italicise_taxonomy.R'><code>R/italicise_taxonomy.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/italicise_taxonomy.R'><code>R/italicise_taxonomy.R</code></a></small>
<div class="hidden name"><code>italicise_taxonomy.Rd</code></div>
</div>

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<h1>Join <a href='microorganisms.html'>microorganisms</a> to a Data Set</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
<div class="hidden name"><code>join.Rd</code></div>
</div>

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<h1>(Key) Antimicrobials for First Weighted Isolates</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/key_antimicrobials.R'><code>R/key_antimicrobials.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/key_antimicrobials.R'><code>R/key_antimicrobials.R</code></a></small>
<div class="hidden name"><code>key_antimicrobials.Rd</code></div>
</div>

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<h1>Kurtosis of the Sample</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/kurtosis.R'><code>R/kurtosis.R</code></a></small>
<div class="hidden name"><code>kurtosis.Rd</code></div>
</div>

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<h1>Lifecycles of Functions in the <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
<div class="hidden name"><code>lifecycle.Rd</code></div>
</div>

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<h1>Vectorised Pattern Matching with Keyboard Shortcut</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/like.R'><code>R/like.R</code></a></small>
<div class="hidden name"><code>like.Rd</code></div>
</div>

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<h1>Determine Multidrug-Resistant Organisms (MDRO)</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mdro.R'><code>R/mdro.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mdro.R'><code>R/mdro.R</code></a></small>
<div class="hidden name"><code>mdro.Rd</code></div>
</div>

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<h1>Data Set with 5,604 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data Set with 70,026 Microorganisms — microorganisms • AMR (for R)</title>
<title>Data Set with 70,760 Microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,8 +48,8 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data Set with 70,026 Microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the microbial taxonomy, last updated in March 2021, of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()." />
<meta property="og:title" content="Data Set with 70,760 Microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<meta name="twitter:card" content="summary_large_image" />
<meta name="twitter:creator" content="@msberends" />
@ -93,7 +93,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
@ -237,13 +237,13 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data Set with 70,026 Microorganisms</h1>
<h1>Data Set with 70,760 Microorganisms</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing the microbial taxonomy, last updated in March 2021, of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href='as.mo.html'>as.mo()</a></code>.</p>
<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href='as.mo.html'>as.mo()</a></code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>microorganisms</span></code></pre></div>
@ -251,7 +251,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 70,026 observations and 16 variables:</p><ul>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 70,760 observations and 16 variables:</p><ul>
<li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
<li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>
@ -269,7 +269,7 @@
<li><p>Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a></p></li>
</ul>
<p>List of Prokaryotic names with Standing in Nomenclature (March 2021) as currently implemented in this <code>AMR</code> package:</p><ul>
<p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul>
<li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
<li><p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <a href='https://doi.org/10.1099/ijsem.0.002786'>10.1099/ijsem.0.002786</a></p></li>
<li><p>Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; doi: <a href='https://doi.org/10.1093/nar/gkt1111'>10.1093/nar/gkt1111</a></p></li>
@ -291,9 +291,10 @@
<p>For convenience, some entries were added manually:</p><ul>
<li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</p></li>
<li><p>3 entries of <em>Trichomonas</em> (<em>Trichomonas vaginalis</em>, and its family and genus)</p></li>
<li><p>1 entry of <em>Candida</em> (<em>Candida krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
<li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>3 entries of <em>Trichomonas</em> (<em>T. vaginalis</em>, and its family and genus)</p></li>
<li><p>1 entry of <em>Candida</em> (<em>C. krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
<li><p>1 entry of <em>Blastocystis</em> (<em>B. hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
</ul>
@ -303,11 +304,11 @@
<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt'>https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a></p></li>
</ul>
<p>The file in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul>
<li><p><a href='https://github.com/msberends/AMR/raw/master/data/microorganisms.rda'>https://github.com/msberends/AMR/raw/master/data/microorganisms.rda</a></p></li>
<li><p><a href='https://github.com/msberends/AMR/raw/main/data/microorganisms.rda'>https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a></p></li>
</ul>
@ -322,7 +323,7 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
@ -349,7 +350,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
</div>
<div class="pkgdown">

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<h1>Data Set with Previously Accepted Taxonomic Names</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.old.Rd</code></div>
</div>

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<div class="page-header">
<h1>Calculate the Matching Score for Microorganisms</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_matching_score.R'><code>R/mo_matching_score.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mo_matching_score.R'><code>R/mo_matching_score.R</code></a></small>
<div class="hidden name"><code>mo_matching_score.Rd</code></div>
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<div class="page-header">
<h1>Get Properties of a Microorganism</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<div class="hidden name"><code>mo_property.Rd</code></div>
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<div class="page-header">
<h1>User-Defined Reference Data Set for Microorganisms</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_source.R'><code>R/mo_source.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mo_source.R'><code>R/mo_source.R</code></a></small>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>

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<div class="page-header">
<h1>Principal Component Analysis (for AMR)</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/pca.R'><code>R/pca.R</code></a></small>
<div class="hidden name"><code>pca.Rd</code></div>
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<div class="page-header">
<h1>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/plot.R'><code>R/plot.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/plot.R'><code>R/plot.R</code></a></small>
<div class="hidden name"><code>plot.Rd</code></div>
</div>

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@ -239,7 +239,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<div class="page-header">
<h1>Calculate Microbial Resistance</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/proportion.R'><code>R/proportion.R</code></a>, <a href='https://github.com/msberends/AMR/blob/main/R/rsi_df.R'><code>R/rsi_df.R</code></a></small>
<div class="hidden name"><code>proportion.Rd</code></div>
</div>

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<div class="page-header">
<h1>Random MIC Values/Disk Zones/RSI Generation</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/random.R'><code>R/random.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/random.R'><code>R/random.R</code></a></small>
<div class="hidden name"><code>random.Rd</code></div>
</div>

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<div class="col-md-9 contents">
<div class="page-header">
<h1>Predict Antimicrobial Resistance</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/resistance_predict.R'><code>R/resistance_predict.R</code></a></small>
<div class="hidden name"><code>resistance_predict.Rd</code></div>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
@ -266,7 +266,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.</p>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt'>https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
@ -292,7 +292,7 @@
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
</div>
<div class="pkgdown">

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@ -239,7 +239,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="col-md-9 contents">
<div class="page-header">
<h1>Skewness of the Sample</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/skewness.R'><code>R/skewness.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/skewness.R'><code>R/skewness.R</code></a></small>
<div class="hidden name"><code>skewness.Rd</code></div>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
</span>
</div>
@ -251,7 +251,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>. This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.) and <code><a href='ab_property.html'>ab_*</a></code> functions (such as <code><a href='ab_property.html'>ab_name()</a></code>, <code><a href='ab_property.html'>ab_group()</a></code>, etc.).</p>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv</a>. This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.) and <code><a href='ab_property.html'>ab_*</a></code> functions (such as <code><a href='ab_property.html'>ab_name()</a></code>, <code><a href='ab_property.html'>ab_group()</a></code>, etc.).</p>
<p>Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese and Spanish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p><h3 class='hasAnchor' id='changing-the-default-language'><a class='anchor' aria-hidden='true' href='#changing-the-default-language'></a>Changing the Default Language</h3>