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(v1.3.0.9014) as.mo() speed improvement

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dr. M.S. (Matthijs) Berends
2020-09-03 12:31:48 +02:00
parent 18e52f2725
commit c4b87fe241
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16
docs/reference/WHONET.html
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@@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with 500 isolates - WHONET example — WHONET" />
<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our example_isolates data set." />
<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -239,7 +239,7 @@
</div>
<div class="ref-description">
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our <a href='example_isolates.html'>example_isolates</a> data set.</p>
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
</div>
<pre class="usage"><span class='kw'>WHONET</span></pre>
@@ -253,10 +253,10 @@
<li><p><code>Organism</code><br /> Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using <code><a href='as.mo.html'>as.mo()</a></code>.</p></li>
<li><p><code>Country</code><br /> Country of origin</p></li>
<li><p><code>Laboratory</code><br /> Name of laboratory</p></li>
<li><p><code>Last name</code><br /> Last name of patient</p></li>
<li><p><code>First name</code><br /> Initial of patient</p></li>
<li><p><code>Sex</code><br /> Gender of patient</p></li>
<li><p><code>Age</code><br /> Age of patient</p></li>
<li><p><code>Last name</code><br /> Fictitious last name of patient</p></li>
<li><p><code>First name</code><br /> Fictitious initial of patient</p></li>
<li><p><code>Sex</code><br /> Fictitious gender of patient</p></li>
<li><p><code>Age</code><br /> Fictitious age of patient</p></li>
<li><p><code>Age category</code><br /> Age group, can also be looked up using <code><a href='age_groups.html'>age_groups()</a></code></p></li>
<li><p><code>Date of admission</code><br /> Date of hospital admission</p></li>
<li><p><code>Specimen date</code><br /> Date when specimen was received at laboratory</p></li>

10
docs/reference/ab_property.html
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Property of an antibiotic — ab_property • AMR (for R)</title>
<title>Get properties of an antibiotic — ab_property • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Property of an antibiotic — ab_property" />
<meta property="og:title" content="Get properties of an antibiotic — ab_property" />
<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of an antibiotic</h1>
<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>
<div class="hidden name"><code>ab_property.Rd</code></div>
</div>

10
docs/reference/as.ab.html
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Transform to antibiotic ID — as.ab • AMR (for R)</title>
<title>Transform input to an antibiotic ID — as.ab • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Transform to antibiotic ID — as.ab" />
<meta property="og:title" content="Transform input to an antibiotic ID — as.ab" />
<meta property="og:description" content="Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to antibiotic ID</h1>
<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>
<div class="hidden name"><code>as.ab.Rd</code></div>
</div>

14
docs/reference/as.disk.html
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Class 'disk' — as.disk • AMR (for R)</title>
<title>Transform input to disk diffusion diameters — as.disk • 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="Class 'disk' — as.disk" />
<meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
<meta property="og:title" content="Transform input to disk diffusion diameters — as.disk" />
<meta property="og:description" content="This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,13 +233,13 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'disk'</h1>
<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>
<div class="hidden name"><code>as.disk.Rd</code></div>
</div>
<div class="ref-description">
<p>This transforms a vector to a new class <code>disk</code>, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<pre class="usage"><span class='fu'>as.disk</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)

14
docs/reference/as.mic.html
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Class 'mic' — as.mic • AMR (for R)</title>
<title>Transform input to minimum inhibitory concentrations — as.mic • 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="Class 'mic' — as.mic" />
<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
<meta property="og:title" content="Transform input to minimum inhibitory concentrations — as.mic" />
<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid minimum inhibitory concentrations (MIC) as levels. Invalid MIC values will be translated as NA with a warning." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,13 +233,13 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'mic'</h1>
<h1>Transform input to minimum inhibitory concentrations</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>
<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 <code><a href='https://rdrr.io/r/base/factor.html'>factor</a></code> with valid MIC values as levels. Invalid MIC values will be translated as <code>NA</code> with a warning.</p>
<p>This transforms a vector to a new class <code>mic</code>, which is an ordered <code><a href='https://rdrr.io/r/base/factor.html'>factor</a></code> with valid minimum inhibitory concentrations (MIC) 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='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)

25
docs/reference/as.mo.html
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Transform to microorganism ID — as.mo • AMR (for R)</title>
<title>Transform input to a microorganism ID — as.mo • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Transform to microorganism ID — as.mo" />
<meta property="og:title" content="Transform input to a microorganism ID — as.mo" />
<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). 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. Please see Examples." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform to microorganism ID</h1>
<h1>Transform input to a microorganism ID</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>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
@@ -248,6 +248,7 @@
Lancefield = <span class='fl'>FALSE</span>,
allow_uncertain = <span class='fl'>TRUE</span>,
reference_df = <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
ignore_pattern = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_ignore_pattern"</span>),
<span class='kw'>...</span>
)
@@ -284,6 +285,10 @@
<th>reference_df</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> to be used for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source()</a></code> and <code><a href='mo_source.html'>get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
</tr>
<tr>
<th>ignore_pattern</th>
<td><p>a regular expression (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the option <code>AMR_ignore_pattern</code>, e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</a></code>.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to functions</p></td>
@@ -299,17 +304,17 @@
<h3>General info</h3>
<p>A microorganism ID from this package (class: <code>mo</code>) typically looks like these examples:</p><pre> Code Full name
<p>A microorganism ID from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre> Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---&gt; subspecies, a 4-5 letter acronym
| | ----&gt; species, a 4-5 letter acronym
| ----&gt; genus, a 5-7 letter acronym
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
| | | \---&gt; subspecies, a 4-5 letter acronym
| | \----&gt; species, a 4-5 letter acronym
| \----&gt; genus, a 5-7 letter acronym
\----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>

10
docs/reference/as.rsi.html
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Class 'rsi' — as.rsi • AMR (for R)</title>
<title>Interpret MIC and disk, or clean raw R/SI data — as.rsi • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:title" content="Interpret MIC and disk, or clean raw R/SI data — as.rsi" />
<meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Values that cannot be interpreted will be returned as NA with a warning." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Class 'rsi'</h1>
<h1>Interpret MIC and disk, or clean raw R/SI data</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
<div class="hidden name"><code>as.rsi.Rd</code></div>
</div>

16
docs/reference/atc_online.html
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@@ -49,8 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
This function requires an internet connection." />
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -83,7 +82,7 @@ This function requires an internet connection." />
</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">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -123,7 +122,7 @@ This function requires an internet connection." />
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -241,7 +240,6 @@ This function requires an internet connection." />
<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.</p>
<p><strong>This function requires an internet connection.</strong></p>
</div>
<pre class="usage"><span class='fu'>atc_online_property</span>(
@@ -309,12 +307,14 @@ This function requires an internet connection." />
<li><p><code>"ml"</code> = milliliter (e.g. eyedrops)</p></li>
</ul>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<p><strong>N.B. This function requires an internet connection and only works if the following packages are installed: <code>curl</code>, <code>rvest</code>, <code>xml2</code>.</strong></p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</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>

5
docs/reference/bug_drug_combinations.html
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@@ -82,7 +82,7 @@
</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">1.3.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -328,7 +328,6 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> calculates the resistance per bug-drug combination. Use <code>combine_IR = FALSE</code> (default) to test R vs. S+I and <code>combine_IR = TRUE</code> to test R+I vs. S.</p>
<p>The language of the output can be overwritten with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale)</a></code>, please see <a href='translate.html'>translate</a>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

489
docs/reference/index.html
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@@ -81,7 +81,7 @@
</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">1.3.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -121,7 +121,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -246,8 +246,8 @@
<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 <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a>.</p></p>
<h2 id="section-background-information-on-included-data" class="hasAnchor"><a href="#section-background-information-on-included-data" class="anchor"></a>Background information on included data</h2>
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
</th>
</tr>
@@ -258,236 +258,35 @@
<tr>
<td>
<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
<p><code><a href="AMR.html">AMR</a></code> </p>
</td>
<td><p>Transform to antibiotic ID</p></td>
<td><p>The <code>AMR</code> Package</p></td>
</tr><tr>
<td>
<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
</td>
<td><p>Class 'disk'</p></td>
<td><p>The Catalogue of Life</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>
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
</td>
<td><p>Class 'mic'</p></td>
<td><p>Version info of included Catalogue of Life</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">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
</td>
<td><p>Transform to microorganism ID</p></td>
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</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>
<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
</td>
<td><p>Class 'rsi'</p></td>
<td><p>Lifecycles of functions in the <code>AMR</code> package</p></td>
</tr><tr>
<td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
</td>
<td><p>Apply EUCAST rules</p></td>
</tr><tr>
<td>
<p><code><a href="ab_from_text.html">ab_from_text()</a></code> </p>
</td>
<td><p>Retrieve antimicrobial drug names and doses from clinical text</p></td>
</tr><tr>
<td>
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
</td>
<td><p>Guess antibiotic column</p></td>
</tr><tr>
<td>
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
</td>
<td><p>User-defined reference data set for microorganisms</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-enhancing-your-data" class="hasAnchor"><a href="#section-enhancing-your-data" class="anchor"></a>Enhancing your data</h2>
<p class="section-desc"><p>Functions to add new data to your existing data, such as the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
</td>
<td><p>Property of an antibiotic</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="age.html">age()</a></code> </p>
</td>
<td><p>Age in years of individuals</p></td>
</tr><tr>
<td>
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
</td>
<td><p>Get ATC properties from WHOCC website</p></td>
</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="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 microorganisms to a data set</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="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">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</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="mo_property.html">mo_name()</a></code> <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_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</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_snomed()</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_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</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="p_symbol.html">p_symbol()</a></code> </p>
</td>
<td><p>Symbol of a p-value</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2>
<p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, or make plots.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
</td>
<td><p>Calculate microbial resistance</p></td>
</tr><tr>
<td>
<p><code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <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 available isolates</p></td>
</tr><tr>
<td>
<p><code><a href="availability.html">availability()</a></code> </p>
</td>
<td><p>Check availability of columns</p></td>
</tr><tr>
<td>
<p><code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i>&lt;bug_drug_combinations&gt;</i>)</a></code> </p>
</td>
<td><p>Determine bug-drug combinations</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> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
</td>
<td><p>Predict antimicrobial resistance</p></td>
</tr><tr>
<td>
<p><code><a href="pca.html">pca()</a></code> </p>
</td>
<td><p>Principal Component Analysis (for AMR)</p></td>
</tr><tr>
<td>
<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> </p>
</td>
<td><p>Antibiotic class selectors</p></td>
</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter isolates on result in antimicrobial class</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 plots with <code>ggplot2</code></p></td>
</tr><tr>
<td>
<p><code><a href="ggplot_pca.html">ggplot_pca()</a></code> </p>
</td>
<td><p>PCA biplot with <code>ggplot2</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="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>Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
@@ -527,7 +326,7 @@
<td>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td>
<td><p>Translation table with 5,583 common microorganism codes</p></td>
<td><p>Data set with 5,583 common microorganism codes</p></td>
</tr><tr>
<td>
@@ -544,8 +343,8 @@
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
<h2 id="section-preparing-data-microorganisms" class="hasAnchor"><a href="#section-preparing-data-microorganisms" class="anchor"></a>Preparing data: microorganisms</h2>
<p class="section-desc"><p>These functions are meant to get taxonomically valid properties of microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganism codes.</p></p>
</th>
</tr>
@@ -556,38 +355,179 @@
<tr>
<td>
<p><code><a href="AMR.html">AMR</a></code> </p>
<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">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
</td>
<td><p>The <code>AMR</code> Package</p></td>
<td><p>Transform input to a microorganism ID</p></td>
</tr><tr>
<td>
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
<p><code><a href="mo_property.html">mo_name()</a></code> <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_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</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_snomed()</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_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>The Catalogue of Life</p></td>
<td><p>Get properties of a microorganism</p></td>
</tr><tr>
<td>
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
</td>
<td><p>Version info of included Catalogue of Life</p></td>
</tr><tr>
<td>
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
</td>
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
</tr><tr>
<td>
<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
</td>
<td><p>Lifecycles of functions in the <code>AMR</code> package</p></td>
<td><p>User-defined reference data set for microorganisms</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-other-functions" class="hasAnchor"><a href="#section-other-functions" class="anchor"></a>Other functions</h2>
<h2 id="section-preparing-data-antibiotics" class="hasAnchor"><a href="#section-preparing-data-antibiotics" class="anchor"></a>Preparing data: antibiotics</h2>
<p class="section-desc"><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
</td>
<td><p>Transform input to an antibiotic ID</p></td>
</tr><tr>
<td>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
</td>
<td><p>Get properties of an antibiotic</p></td>
</tr><tr>
<td>
<p><code><a href="ab_from_text.html">ab_from_text()</a></code> </p>
</td>
<td><p>Retrieve antimicrobial drug names and doses from clinical text</p></td>
</tr><tr>
<td>
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
</td>
<td><p>Get ATC properties from WHOCC website</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-preparing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-preparing-data-antimicrobial-resistance" class="anchor"></a>Preparing data: antimicrobial resistance</h2>
<p class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
</th>
</tr>
</tbody><tbody>
<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>Interpret MIC and disk, or clean raw R/SI data</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>Transform input to minimum inhibitory concentrations</p></td>
</tr><tr>
<td>
<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
</td>
<td><p>Transform input to disk diffusion diameters</p></td>
</tr><tr>
<td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
</td>
<td><p>Apply EUCAST rules</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-analysing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-analysing-data-antimicrobial-resistance" class="anchor"></a>Analysing data: antimicrobial resistance</h2>
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
</td>
<td><p>Calculate microbial resistance</p></td>
</tr><tr>
<td>
<p><code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <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 available isolates</p></td>
</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="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="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">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</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="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 plots with <code>ggplot2</code></p></td>
</tr><tr>
<td>
<p><code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i>&lt;bug_drug_combinations&gt;</i>)</a></code> </p>
</td>
<td><p>Determine bug-drug combinations</p></td>
</tr><tr>
<td>
<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> </p>
</td>
<td><p>Antibiotic class selectors</p></td>
</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter isolates on result in antimicrobial class</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> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
</td>
<td><p>Predict antimicrobial resistance</p></td>
</tr><tr>
<td>
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
</td>
<td><p>Guess antibiotic column</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-other-miscellaneous-functions" class="hasAnchor"><a href="#section-other-miscellaneous-functions" class="anchor"></a>Other: miscellaneous functions</h2>
<p class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></p>
</th>
</tr>
@@ -608,11 +548,84 @@
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
</td>
<td><p>Pattern Matching</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="age.html">age()</a></code> </p>
</td>
<td><p>Age in years of individuals</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 microorganisms to a data set</p></td>
</tr><tr>
<td>
<p><code><a href="availability.html">availability()</a></code> </p>
</td>
<td><p>Check availability of columns</p></td>
</tr><tr>
<td>
<p><code><a href="pca.html">pca()</a></code> </p>
</td>
<td><p>Principal Component Analysis (for AMR)</p></td>
</tr><tr>
<td>
<p><code><a href="ggplot_pca.html">ggplot_pca()</a></code> </p>
</td>
<td><p>PCA biplot with <code>ggplot2</code></p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
<h2 id="section-other-statistical-tests" class="hasAnchor"><a href="#section-other-statistical-tests" class="anchor"></a>Other: statistical tests</h2>
<p class="section-desc"><p>Some statistical tests or methods are not part of base R and are added to this package for convenience.</p></p>
</th>
</tr>
</tbody><tbody>
<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="kurtosis.html">kurtosis()</a></code> </p>
</td>
<td><p>Kurtosis of the sample</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><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>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-other-deprecated-functions" class="hasAnchor"><a href="#section-other-deprecated-functions" class="anchor"></a>Other: deprecated functions</h2>
<p class="section-desc"><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p></p>
</th>
</tr>

8
docs/reference/like.html
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@@ -82,7 +82,7 @@
</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">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -274,7 +274,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>%like%</code> function:</p><ul>
<li><p>Is case insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li>
<li><p>Is case-insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li>
<li><p>Supports multiple patterns</p></li>
<li><p>Checks if <code>pattern</code> is a regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed</p></li>
<li><p>Tries again with <code>perl = TRUE</code> if regex fails</p></li>
@@ -295,7 +295,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</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://rdrr.io/r/base/grep.html'>base::grep()</a></code></p></div>
<div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>grep()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># simple test</span>

10
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Translation table with 5,583 common microorganism codes — microorganisms.codes • AMR (for R)</title>
<title>Data set with 5,583 common microorganism codes — microorganisms.codes • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Translation table with 5,583 common microorganism codes — microorganisms.codes" />
<meta property="og:title" content="Data set with 5,583 common microorganism codes — microorganisms.codes" />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Translation table with 5,583 common microorganism codes</h1>
<h1>Data set with 5,583 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>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
</div>

18
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@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Property of a microorganism — mo_property • AMR (for R)</title>
<title>Get properties of a microorganism — mo_property • 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="Property of a microorganism — mo_property" />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
<meta property="og:title" content="Get properties of a microorganism — mo_property" />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@@ -82,7 +82,7 @@
</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">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -233,13 +233,13 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Property of a microorganism</h1>
<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>
<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. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. Please see <em>Examples</em>.</p>
<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. Please see <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>mo_name</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
@@ -299,11 +299,11 @@
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption("AMR_locale")</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale = "de")</a></code>, see <a href='translate.html'>translate</a>. 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>
<td><p>other parameters passed on to <code><a href='as.mo.html'>as.mo()</a></code>, such as 'allow_uncertain' and 'ignore_pattern'</p></td>
</tr>
<tr>
<th>open</th>

11
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@@ -82,7 +82,7 @@
</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">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
</span>
</div>
@@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@@ -247,11 +247,10 @@
<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>.</p>
<p>Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.</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/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_property()</a></code> functions (<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.).</p>
<p>Currently supported languages are: Dutch, English, French, German, Italian, Portuguese, Spanish. Please note that currently not 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>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property()</a></code> functions (<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.).</p>
<p>The system language will be used at default, if that language is supported. The system language can be overwritten with <code><a href='https://rdrr.io/r/base/Sys.setenv.html'>Sys.setenv(AMR_locale = yourlanguage)</a></code>.</p>
<p>The system language will be used at default (as returned by <code><a href='https://rdrr.io/r/base/locales.html'>Sys.getlocale()</a></code>), if that language is supported. The language to be used can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale = "de")</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>